GemFire transactions do not write atomically to disk. So, if a member crashes while commiting a transaction (say only 3 of the 5 transactional operations had been persisted), on recovery the entire transaction might not be recovered. Hence, transactions on persistent regions are not allowed by default. GemFire throws an UnsupportedOperationException.
ALLOW_PERSISTENT_TRANSACTIONS allows you to get around the UnsupportedOperationException.
It might be ok to use this flag if you have redundancy for the region along with persistence, and all members hosting this region do not crash simultaneously. If a member crashes while commiting a transaction, the transaction still could have been commited by another member in the system. When this crashed member comes back up again, it is told that it has an older persistence file, and it fetches the complete image from the other member.