EPDM roof

Hopefully yours is aluminum framed like mine is, that's the only reason why it didn't completely collapse, haha those AC units are up to 200lb. The contact cement has no reaction with the EPDM rubber and you can buy Liquid Rubber in 1 and 5 gallon cans in white as well. You could use a filler for your seams but I'm always weary of cracking, hence the eternabond tape, it you go with the liner that would of course eliminate that issue.
From what I see in your pics, the repair is definitely worth doing. Another tip as well, I can't tell from the pics but often times with these older C's the weight of the AC unit will tend to sag your roof a bit especially after water damage, but even from just plain old metal fatigue if you have aluminum rafters. Other than having a cambered roof; which yours does not appear to have you can fix by elevating it with a sheet of 7/8's OSB or whatever you prefer. The AC wire harness should have plenty of wiggle room as your only adding an additional inch to elevate the unit above the water line should your nice new roof sag and pool once complete otherwise, been there done that. I used a full sheet of OSB and it worked fine. Sure it adds weight to rig but only 80lbs or so. Well worth it for a five year investment. Mines a 30' 1993 and my roof has done great since then and will last another five years no problem.