To answer your questions in relative order:

1) I don't think you can upgrade to the Collector's Edition from the Standard version until Shadowbringers officially releases on July 2nd; that being said, I presume that it'll be available as soon as the expansion officially launches. If you want to purchase it now, the digital Collector's Edition is available through SE's digital store.

2) Most old content is still available for play in one way or another. Pretty much all casual instanced content - dungeons, normal/hard trials, raids - have roulettes that keep the queues filled, and the harder content (EX trials, savage raids and the Coil raids) can usually be done through Party Finder without too much trouble, though you may have to do them unsynced; you'll still be able to get mounts/emotes/etc. that way, though. Gold Saucer stuff mostly sticks around aside from some GATE events, I believe (and I could be wrong about that, too - I don't spend much time in the Gold Saucer). Housing is unfortunately more of a problem; if you're on Balmung, you probably won't be able to get a house, though apartments are plentiful enough that getting one of those shouldn't be too much of an issue (though Balmung's permanent congested status may make it more difficult than another server). Airship stuff is usually done through Free Companies, so you'll need to join one if you haven't already.

3) Balmung is still considered to be a major RP server and has been permanently congested for a very long time, though there are definitely others as well; the new Crystal data center that Balmung is now on is often stereotyped as the "RP data center", though that should be taken with a healthy level of skepticism as with all stereotypes.

4) I don't really know much about the 'marks' of characters carried over from 1.0, but aside from subscriber bonuses accounts don't get equivalent marks simply due to age. That being said, Fantasias shouldn't remove Legacy markers, I believe.

5) I don't think anything on Mogstation is obtainable in-game; that being said, a lot of the stuff on there are items from previous seasonal events that are no longer obtainable, exclusive items from real-world events like Fanfest, or items from the Chinese/Korean version of the game that were ported over to this version, so that isn't that different. It's also important to note that the amount of mounts/emotes/glam outfits/etc. available in-game vastly outweighs what is available on Mogstation, so don't feel like you can't get anything in-game. The character-specific thing is a little annoying, but that's about the only problem I have with Mogstation's stuff.
5b) As far as I'm aware, there aren't any plans to offer other methods of obtaining most of the Mogstation stuff; it sounds like the other person was probably just passing on a rumor.