I suppose that in the sagas that I will be running, I will simply stick to a variant of the early proposal from ErikT: if the target of Perdo can be destroyed by mundane ways, then the default duration of the spell is Momentary, and this means "permanent"; if the target of Perdo cannot be destroyed by mundane ways, then the default duration of the spell is Momentary, and this means "during one round, and automatically restores to its previous state after that".
It does not solve all the questions about PeVi effects, but at least it would mean that "Reduce the casting total" is of the second category while "Reduce the duration of an Arcane Connection" is of the first category.
My suggestion was that it would be research to be able to have temporary destruction as an option, rather than the only way to use Perdo. That feels like a small/medium breakthrough to me.
I've played a character with Harmless Magic, it was fun and frustrating at times. There were some advantages, a number of disadvantages.
You aren't 'given the ability to make temporary Perdo and lose the ability for permanent', your spells get fundamentally changed.
If you take the interpretation that Temporary Destruction is possible normally - A House Rule I think is cool, but feel is very much a HR - then you need to figure out how that affects spells when shared. By common interpretation, if I take a Break a Leg spell and sell a copy to TemPerdo, the same spell does notably different things. If TemPerdo designs Knock Down a Wall, then a normal magus learning that spell from him has the wall stay fallen, not bounce back up. It's a fundamental change of magic, rather than a new option.
I'm actually very curious as to the canonical example where you get to decide the shape that way - I thought it was based on the actual effect. (MuTe to turn rock to clay and reshape it by hand, it stays the new shape, MuTe to turn a rock into a differently shaped rock, it turns back.)
FWIW, I'd say one simple thing: Permanent Perdo Magic is too (very, in fact) useful and powerful, as DEO perfectly illustrates. That is why Harmless Magic is a flaw
Muto works pretty well for temporary destructions of anything actually. As someone who picked Harmless Magic a few times, if there's anything I can tell you is that I don't see the option as a real boon (even if designing the temporary perdo spells amuses me), because the base guideline are calibrated in such a way that the temporary perdo spell isn't more efficient as an equivalent Muto might be. I did a PeTe 15 spell in a game - Base 3, +1 stone, +1 touch, +1 part, +1 size - to temporarily remove a wall. Which another mage could have done as a MuTe(Au) spell of the same level while retaining the ability to merely delete the wall, or to then move/destroy the air as an added option. It looks like a boon on surface, but it's a trap, because it makes you want to develop a technique you suck at (Perdo) instead of putting the xp in a technique that's broadly useful (Muto). Want to temporarily erase a memory? Just change its contents... It's easier too. I don't think I've found a single case where an effect I wanted to do temporary destruction resulted in the gain of a magnitude. The idea of something temporarily not existing amuses me... But whether it's really useful is a different question.