As for the mod breaking quests you just have to use common sense, the same as we did way back in Daggerfall Morrowind. Mark/Recall has always been something that could break scripted events and quests, even when it was an official spell featured in the game by Beth them selves.

Its pretty much a good idea to not use it if your Currently in any kind of scripted event, quest, dungeon or any setting where the game has you "locked" into a situation and wants you resolve it right at that very moment. If you are locked into a dungeon because of a major quest line or something or ported to a different realm or following/leading a follower to a quest objective its really not a good idea to use these spells to escape, but if your just on a side quest or misq quest or pretty much any hunt and peck quest that you could normally ignore and leave in your journal shouldn't be effected by these spells any more than they are effected by you ignoring them leaving them in your journal.

I pretty much only use it while exploring the game and mucking around etc etc, and would never use it if i was actively on a quest.

Just a thought, maybe also have A Prayer to Talos, which would transport you to the nearest Talos shrine? Of course, it would only be possible to buy it from priests of Talos - if you had a high enough speechcraft or reputation with them to persuade them that you wouldn't get them in trouble .