Can I do geometric parametric study with OpenStudio? Can jEPlus intersect and match surfaces?

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Yes, with measures you can do parametric studies on almost anything. Check out OS Spreadsheet

For jEPlus you may find it easier to have different base models with just the geometry saved in IMF files. You would then use jEPlus to set a value that selects which geometry file to include.

Something like:

##include @@PathToGeometryIMF@@

This is by far the easiest approach if you need to intersect and match surfaces as jEPlus can't do that.

For simpler geometries, it's certainly possible to do as @David Goldwasser suggests and use scaling factors (I've done this before to set the area of PV panels or to adjust window to wall ratios using jEPLus and EPMacro). The maths might get a little messy depending on how complex your geometry is but if it's just stretching on the x- and y-axes then it's not hard at all.

If jEPlus isn't finding any jobs then I'd suggest simplifying things to see if you can isolate the problem that way as it ought to work.

Yes OpenStudio can do parametric studies where we alter geometry. We have internally used a measure with a multiplier for x and y to scale the entire building. If you want to scale individual zones, of course this is more complex, to make sure zones fit together if they don't scale by the same factor. Rather than changing the geometry you could also change the zone multiplier, but if you are trying to look at daylighting impact of larger spaces, then you probably want the actually geometry deeper. The zone multiplier also wont change the surface area to volume ratio of the building.

I'll let someone else speak to best approach with jEPlus.