I would ask that they be sealed. 

A very thorough cleaning and sealing of all surfaces should bring the property to a like new condition. 

I went and bought a vinyl garage door frame seal.

As a result we were left to foot the bill for $2300 of pest control and we have to seal all of the subfloors to block the dog urine odor.I feel that it is only fair to revise my reference for these tenants with their new landlord, and to let them know to inspect for bugs, since they are most likely taking up residence there now.

Also, if you seal the grout(comes in a squeeze bottle, 2-3 coats) it will stay clean/cleanable.

Removing it is tedious, and can leave the underlying walls / ceilings in poor shape with gouges and other damage caused by the removal process, particularly if the walls / ceilings weren't sealed and sized before the paper went up. 

As in the deal is signed, sealed and delivered and you've been cut out?

Contractor said its normal, but would at not cost to me come back out in two weeks and put a topcoat/seal on it, covering everything in black to make it look uniform. 

Epoxy putty, flex seal, whatever you use can patch it for a short while but the real permanent fix is to remove the stretch of pipe which involves removing walls on a tiled bathroom.However, even though the drain line drains from my kitchen, it is located in a wall cavity which separates two units.

I just signed up to re-invest some of that into a local program where the utility company subsidizes insulation, and air sealing.