That sounds like it should be a bug. Doesn't that make the Unlock spell rather pointless if mages can blow apart locked doors and containers without point-investment or equipment penalty?
Maybe a dev could answer that, but I'm not getting the impression that magic being able to open doors and such is a bug.
You seem to think that having multiple solutions to opening a door is an error, when it seems more likely to be a design choice for roleplaying purposes.
I'm struggling to understand what the drawback of a low Repair skill is with this setup. Let's say I have a magical piece of equipment and a Repair skill of 1. So, I repair the item to 40% of it's maximum durability. Ok.. so when that 40% wears out I just repair it back up again? Seems like I just have to repair more often and that's it. What's my incentive to continue raising my Repair skill?
All right, maybe it could be impossible to repair Tier 3+ items with Repair 1, only Tier 1/2 (Normal/Magic [Blue]) items could be repaired, and the Tier 2 ones a lot less. With Repair 2, you can now repair Rare items [Green], and so on.
But if you try and go much farther in forbidding what you can repair, here's my concern: it can take several levels just to reach Rank 3 in a ability - level 5 at the earliest. By that time you've probably already got a bunch of Tier 2 and a couple Tier 3 items. Given the limited number of ability points, is it likely that you have spent them all on a support ability like Repair by character level 5? Not really.
Repair is not a primary ability and never will be, it's a support or roleplaying skill.
That means that realistically, it'll be a few more levels before you have enough points to throw towards abilities like Repair. During that time, you'll have accumulated even more gear, which will require higher levels in repair just to touch. If low levels in Repair are worthless because the majority of your gear is so advanced you need to have NPC's repair it anyway, people have no reason to invest in it.