I once had a putt land in the basket...and then fall through the bottom of the basket back onto the ground...in a tournament. We all counted it as a made putt, but yes the course is FAR and away better that it once was.
It shouldn't have counted.
802.05 Holing Out
Basket Targets: In order to hole out, the thrower must release the disc and it must come to rest supported by the chains and/or the inner cylinder (bottom and inside wall) of the tray. It may be additionally supported by the pole. A disc that enters the target below the top of the tray or above the bottom of the chain support is not holed out.
I would venture to guess you are not reading the wording correctly as it did NOT enter below the top of the tray OR above the bottom of the chain support. It entered the basket correctly and would've come to rest had the basket been in good repair. There was simply a metal bar missing on the bottom which would've allowed the disc to come to rest. As such, yes, it counts.