Certain characters do have ways around it. Rogue-Bot can drop a Robo-Bomb onto it, Fairy can teleport around it or put a crystal ball on it. Though the ways around them are often long and involve a lot of back-tracking, they usually do exist.
Jumping head-first into such a portal has unpredictable results, I agree, which sometimes do just mean time 'wasted'. But there's also the chance that they drop you into a highly challenging encounter, so 'guaranteed' success in the game means always preparing for the worst and hoping for the best. This introduces a lot of choices (do I want to cast Martyrin' / Purify first, just in case? Should I switch to leather to help in running out of danger?).
Even when a teleport drops you to an empty room and forces you to backtrack a lot, this creates strategy in other parts of the game. It tightens your food resources and requires a keener eye towards efficient play in other parts of the game.
I understand that it is one of the few places in 100 Rogues where the game removes control from the player. We do feel that these instances strengthen the challenge and replayability of the game significantly.
As for checking the version number, you can always right-click the app in iTunes. I believe the context-menu option is 'get info', which will give you versioning information.