It is a bit convoluted and it seems I may not have rememberd the training problem for GF 3 quite right. It seems canisters and books (and quest rewards?) may indeed count as training when trainers are concerend (I'm in GF5 and havent played for 3 months now so details get mixed up in my head). According what I read, you should train skill first before taking any canisters, reading books or spending skills points (obviously this is not always possible especially in first play thru without help of walkthru). The creation skills (and lesser extend with spells) as you may already know that you get better version of creation at level 3 of particular create creation skill (cryora at level 3 of create fyora skill and so forth). So if you've spend all the alternate medhods of gaining skills first you may not even be able to gain third level of a skill. The general advice is to save before completing quests (when you go get reward), reading books or using canisters to see what they give and reload if it's something you've yet to learn thru training.

As for canister maddness, I did not find conclusive number (some say it's 6-7 others 10) but it seems to have limited effect on game play itself (mainly some minor alterations to flavor and conversation texts) and primarily alters the ending and mainly only your part of it.

This is one of the grievances I have with GF series. All ways to gain skill should be threated as egual and I should not have to hold of spending skills, reading books or using canisters out of fear I may not be able to train with trainer I may meet later. Other annoyance is that not all stats are shown, especially on creations so you are left quessing what some thing give (So spell protects me. How and how much? Does it just make me harder to hit or does it also reduce damage I make?).

So my advice is to read thru general info part of a walkthru before starting any of GF games.