That would be great, I use MOE - Main Quest Delayer, which puts the main quest completely on hold until the player actually gets put in prison(!) In this way, one can spend a lot of time ignoring the main quest (and presumably never going near any MQ01 stages).
MQ01 is not really the main quest. MQ01 is the tutorial quest, the quest that is responsible for popping up various tutorial windows, and stage 90 is the one that pops up an explanation of the quest arrow as soon as you leave the sewer. I know that many players tend to start games from old saves just before leaving the sewer, as that is the last time you can freely change all stats, so my main focus is to be compatible with games that start completely new, or from a save within the sewer.
My hope was that alternate start mods set those tutorial stages to done pretty soon to prevent the tutorial windows from popping up, in which case doing it this way would work with them. But I guess I will need to hook into each of them individually if not - which is why I hope to get some help from people having such ones installed and a bit of a knowledge with the CS.
Alternative Start by Robert Evrae.esp
This one may have an issue with your toggle then. If you are relying on the game going through stage 90, this alt start mod doesn't ever set stage 90. It sets stage 88 and then stage 100. I'll double check it later, because the chargen sequence is hard to follow so I may be missing something.
Thanks. I appreciate if you do so. I need to be able to check for something that changes state at the moment I should hide the markers. In vanilla, stage 90 seemed the best, but I can check for additional stages, like stage 100.
Nonetheless you have a fantastic mod and I'm using and enjoying it actively. However just off the top of my head, I haven't been able to distinguish 'oblivion gate closed' markers from the open version. All my gates show a normal-looking gate marker (the gate archway symbol). However I have already completed the main quest so maybe what I am seeing is the gate closed marker...? I don't remember tweaking a setting for it in the INI, but I didn't see one to tweak either.
Thanks

Tere is one ini tweak for it:
; Set how Oblivion gate markers are handled:; 0: You can manually change the marker between open and closed; 1: The markers automatically change between open and closed; 2: The markers automatically disappear when gates are closedset tnoMMO.gateMode to 1
If this is set to 0, all your gates will be as normal until you manual edit a gate's state (by clicking on it in the world map). But if 1, it should check all your gates at game load and set them to closed if you're finished with the main quest. And the two different states should be distuingishable. I have now added an http://www.tesnexus.com/downloads/file.php?id=26389 showing the two states for three different icon types.
What about the priory (or whatever) where you are told to go for the main quest? Doesn't Baurus mark your map with that one for you when the quest is given? I would think that should be left on the map in an unvisited state, same as any other quest in the game where someone marks your map for you.
Good point. I can check the state of MQ02 and set that map marker to visible after hiding the markers. As for any other quest given before this, there are none I know of. If someone reports any such mod-added quests, I can probably make sure to make its marker visible though.