Can we generate the BOM as per creo model tree for WTpart

Yes, that is how is works OOTB but some conditions apply. Each CAD model needs a WTPart associated to it as owner or image link. This too is how it works, it should generate a WTPart as owner link and create a BOM structure if that is a CAD assembly.  Is there something different than what you are seeing? Perhaps we should compare preferences.

When you have similar models which are different variants, so one starts using simplified representation for creating different assembly drawings, how is this catered for in Windchill, WT models, Simplfied Reps and getting individual BOM's? Can this be done. Or do each variant need to have their own dedicate assembly's with WT's and only then BOM's can be derived?

My company is planning to get the BOM's via Windchill for each variant, but there are 20 variants all in one assembly, so 20 simplified reps have been made making 20 drawings. Can BOM's still be acquired for each assembly via Windchill?