Regarding your 16" rims/tires, if those do not fit in the frunk properly they are most likely far oversized. I've used 195/50/15 and 205/50/15 and have had no problem storing one in the frunk if needed. The oem 14" space saver tire is actually a bit smaller in diameter than even oem 185/60/14 tires, I think, and it still works fine. 195/50/15 tires are generally the same diameter as the oem setup, and 205/50/15 tires are just slightly larger. Not sure I would be too worried about matching a space saver with either one, but possibly depends upon the lsd and how sensitive it is. 15" tires will perform far better than 14" tires, plus I think the rim size looks much better than 16" on a MKI.
As for the blocked air vents, maybe that is a temporary thing they do in some places, but if you want any fresh air through your vents, how can that happen with those in place?