Yup, sometimes I have a feeling development would go much smoother and with a lot less bugs if they decided to follow the tabletop guidelines: no party members change during adventure, no repeating completed scenarios, no saving individual characters (only complete parties)
Actually, just about all of those things are permissible under tabletop rules. It is just that set-up is such a pain that people rarely seem to want to replay scenarios when they can just keep pushing on ahead.
The rulebook honestly doesn't have as much to say about what happens "between" games, but the two rules do apply.
You must ... complete [a scenario] successfully before you can attempt the next scenario.
You may not earn the reward from a given scenario, adventure, or Adventure Path more than once unless the reward specifically tells you otherwise.
When asked to clarify, the creators have replied that it is perfectly okay to replay scenarios. If you're leveling up a new adventurer, or want to grind for cards, the only restriction is that a character (not the party or the player) cannot receive scenario rewards more than once.
As far as splitting and combining parties, Class Decks were partly designed to facility organized play and make it easier to swap characters in and out of games.
All the things you listed are technically "rules legal", but just cumbersome to exploit in tabletop. The app just makes it really easy to experiment with the rules and find ways to power-level characters without the threat of permadeath.
Optional permadeath is probably the biggest change that allows for rules shenanigans. You might be a little more hesitant to replay "Here Comes the Flood" over and over again to collect allies if there was a chance that one of those Nightbelly Boas could kill off your AD6 Ezren.