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Please forgive the lengthy response in attempt to answer my own question, but I want to do so to draw out some constructive feedback from the community:

Here's what I decided to try, but I am unsatisfied with the output results for my boiler and for my DX cooling coil which appear to come out undersized based on the constraints I have selected. I’ll explain more at the end. If others have a different opinion on how to approach this model, please chime in (note that if I do not mention a particular input field below it means I left the Openstudio default choices as is): I modeled two laboratory spaces each with 8 VAV fume hoods and assigned each space to its own thermal zone. I chose to use the Fan:ZoneExhaust, one per lab space. I made an hourly schedule for fume exhaust utilization as a percentage of total exhaust flow. Since each hood is worth 1200 cfm of exhaust at full flow and I have 8 hoods, I set the Maximum Flow Rate for each zone exhaust fan to 9600 cfm. I assigned my fume exhaust utilization schedule as "Flow Fraction Schedule Name", selected Coupled and Always On Discrete for my availability schedule. I left the "Balanced Exhaust Fraction Schedule Name" unassigned as my understanding is that if this field is left alone, E+ will attempt to balance the zone exhaust with supply air (Is this correct?).

Next, I assigned my two lab zones to a Packaged DX Rooftop VAV with Reheat.
For the Controller:OutdoorAir Object I made the following choices: “Minimum Outdoor Air Flow Rate”= Autosized, “Maximum Outdoor Air Flow Rate” = Autosized, “Economizer Control Type” = NoEconomizer, “Economizer Control Action Type”=ModulateFlow, “Lockout Type”=NoLockout, “Minimum Limit Type”=ProportionalMinimum, “Minimum Outdoor Schedule Name”=Always On Discrete, For both “Minimum Fraction of Outdoor Air Schedule Name” and “Maximum Fraction of Outdoor Air Schedule Name” I selected Always On Discrete in an attempt to force my outdoor air fraction to 100% OA at all times since my AHU in reality will be a VAV 100% OA unit (no return duct) that tracks my zone fume exhaust flow rate.
For the AirLoopHVAC Object, I made the following choices: “Availability Schedule”=Always On Discrete because my AHU will remain on 24/7 (note that for my Fan:ZoneExhaust I selected Coupled and also selected Always On Discrete). For “Design Supply Air Flow Rate” I selected Autosized. This is my attempt at letting E+ match the supply airflow rate to the Fan:ZoneExhaust rate that is dependant on time of day based on my use of the Flow Fraction Schedule that I made for my fume hood usage.

For the Sizing:System Object under AirLoopHVAC for my Packaged DX Rooftop VAV with Reheat unit, I made the following choices: “Type of Load to Size On”=VentilationRequirement (I selected this as my first choice because I believe this must be the right selection for a fume exhaust-driven HVAC system, but I would like to hear some feedback on this from more experienced users, please.), “Design Outdoor Air Flow Rate”=Autosized (not sure if I should input a numerical value here or not. See below for how I specified my DesignSpecification:OutdoorAir for my lab space type), “Sizing Option”=NonCoincident (because I want to size my AHU for the sum of both of my lab spaces peak flows), for both “100% Outdoor Air in Cooling” and “100% Outdoor Air in Heating” I selected Yes, for both “Cooling Design Air Flow Method” and “Heating Design Air Flow Method” I selected Flow/System and input the value of 19,200 cfm because that is 2 x 9600 cfm - the maximum expected exhaust flowrate for each lab zone when all fume hoods are 100% utilized, For both “Cooling Design Capacity Method” and “Heating Design Capacity Method” I selected CoolingDesignCapacity and HeatingDesignCapacity, respectively, and selected Autosized for “Cooling Design Capacity” and “Heating Design Capacity”, lastly for “Central Cooling Capacity Control Method” I selected VT. Under DesignSpecification:OutdoorAir under the Space Types tab for my laboratory space type, I made the following choices: “Outdoor Air Method”=Sum, “Outdoor Air per Person”=0, “Outdoor Air Flow per Floor Area”=0, “Outdoor Air Flow Rate”=9600 cfm (because I am attempting to match my zone outdoor air flow to my exhaust flow neglecting infiltration - for now), for “Outdoor Air Flow Rate Fraction Schedule Name” I selected my fume hood usage schedule. Under AirTerminal:SingleDuct:VAV:Reheat I made the following choices (there are two of these, one per lab space and I made the same selections for both): “Maximum Air Flow Rate”=Autosized, “Zone Minimum Air Flow Input Method”=Scheduled, “Minimum Air Flow Fraction Schedule Name”=(my fume hood usage schedule”), “Maximum Hot Water or Steam Flow Rate”=Autosized.

All of my air systems appear to be correctly sized per the maximum cfm constraints that I input, but my boiler and my DX cooling coil are very undersized. The boiler is the easiest to explain because it should be sized based on dry bulb temperatures-only. My winter design outdoor air temperature is 30.2 degrees F and my space design heating temperature is 70 degrees F. My supply airflow rate for my two lab zones with the 1.15 heating sizing factor is coming out at 22080 cfm (9600 cfm x 2 x 1.15). I specified my hot water heating coil (Coil:Heating:Water) inside my AHU to have a Rated Outlet Air Temperature of 58 degrees F and I specified my zone reheat coils to have a Rated Inlet Air Temperature of 58 degrees F and a Rated Outlet Air Temperature of 90 degrees F. So my overall sizing delta T for heating should be 59.8 degrees F (from 30.2 degrees F to 90 degrees F) from the Outdoor Air inlet to my supply outlet into the zone. My estimated boiler load based on these parameters is 1,426,014 BTUH or (418,186 Watts), however the boiler sizing calculation from E+ is only 89231 Watts. A significant difference.

My DX coiling coil nominal total capacity from E+ is 223,418 Watts, but my estimate using psychrometric analysis came out to 314,723 Watts (not as bad as my boiler in comparison, but still undersized). Because my lab system flowrate is being constrained by fume hoods, it is relatively easy for me to size the system components outside of Openstudio/E+ (which is what I normally do anyway). However without a way to ensure that I’m getting expected sizing results out of E+, it calls into question whether or not I am correctly building my energy model parameters for the simulation. Is there a way to get E+ output which explains the cooling and heating loads due to ventilation both for sizing and for the simulation? I am afraid that my Outdoor Air % is being treated by E+ as less than 100% as it is the most logical explanation for why my boiler and DX cooling sizing loads are low.

Thanks for reading this far, if you did. I would appreciate any feedback.