"Tilia is alive! I think she's the one next to the tree in the morning, near the portal, right?" Yes. If you do her events, you eventually get a chance to either remove one of TFs or to get bigger boobs/smaller dick (depending on your breast size, nipple TF and lots of RNG)
"I didn't save her, but that's very strange. Usually, the game lets you wander after you defeat the magico, so I just wanted to go there after that, but she disappeared, Isabelle got angry etc."
Yeaaa, the game really doesn't make it obvious you need to do the Tree dungeon before Earth trip...Or that Tree dungeon even exists and you HAVE to get the breast TFs from Tilia to get into it. This is probably the least thought out part of the game.
"Is the main camp building the one where Marianne and Isabelle live? Because I found some magazines in Natalie's closet during the panties quest, but nothing happened." Yes. The magazines in Natalie's closet are unrelated.
"I haven't found the book in Phyre's tower, but I guess I could still find it." It's in the room next to the core basement. Not sure if you can pick it up in any order, but you probably can.
"When I blew up Yoshida's room door, Marianne punished me, so I couldn't enter it." That's totally on you, explosives are obviously the worst possible way to do that.
"That's just one more interaction, so I could go to two, but not to the three needed for the succubus content?
" Save editing is always a thing. Just make sure the editor can toggle flags and not just variables.
"I have never used the mana burst outside of combat, so I guess it could be my 6th!" That shouldn't be possible tho. There are TOTAL of 6 ways to get smaller dick and you missed Tilia's one at least. If you're at stage 5, you should have neither dick nor vagina.
"Yes, I got mail bombed twice. The first time it just exploded, while the 2nd time it was with the mailwoman."
Second one is a quest. Usually, Tilia tells you where to go, but maybe someone else can do that too. Not sure if just going to the place yourself is gonna progress it.