It seems extremely costly if I were to run separate ductwork and supply and returns for each unit... can someone walk me through how they're making this work.Thanks,Sean

Sometimes I think the ductwork/age of house etc. have so much to do with it.

Had to get a special cleaning for the duct work and also ran an ozone generator a ton. 

As long as you have ductwork in place, I strongly recommend NOT putting in A/C and instead going with a heat pump.

I just finsihed a scope of work for a single family flip that involves rough plubming, rough electrical, minor duct work, a small section of load bearing wall removal, and a conversion of a haff bath to a full (along with a bunch of cosmetic work).

I assume all the ductwork is already in if there is a boiler.

What has worked for me was taking it down to the studs, paint anything that still smells with Kilz, put in new sub-floors, sheetrock on walls and ceilings, and clean/replace ductwork.  

You WILL need to paint everything including walls, ceilings, (and floors in the grow room , clean the furnace, clean the ductwork, and wash all other non-paintable surfaces with a special cleaner to rid the house of the smell after they leave.Im just finally coming to the end of this process and am putting an ozone machine now because there is still a tiny faint smell when i first open the side door.

I talked to the HVAC guy who put the ventless units in this before we purchased and he seemed like there weren't a lot of options without getting into some crazy expensive systems since there is no ductwork.  

An improvement adds to the value of property, prolongs its useful life, or adapts it to new uses.Some examples of improvements include: a new deck, storm windows/doors, wall-to-wall carpeting, duct work, and insullationAs you noted, even items that would usually be treated as repairs and maintenance are treated as an improvement if incurred while "getting the property ready for use."