I didn't read posts yet, but here's how I solved my tome problems.
First, create a Blessed Book, which hills 1,000 spell levels. At 20th level, my gm allowed me to craft a Tome from Rise if the Landlords which has infinite pages.
Bookplate of Recalling for just 1, 000gp Is a perfect Item combined with Bookmark of Deception makes your main tome always available and super safe.
Edit:
Note the premade spelltomes in Ultimate Magic doesn't say anything that you use those books only after copying them. In fact, a bunch of them grant bonuses for using them directly when preparing.
Rise of the Landlords?
Sounds like an adventure path for little golarion children playing papers and paychecks!
Autocorrect on tablet, while funny, it was meant tome Runelords.
At the bare minimum, I like to put all my actual spells into travelling spellbooks that I keep in my pack, while wearing a full sized and fairly ornate (more expensive for the sheer purpose of looking fancier) but completely empty spellbook out in the open. That way if some theif decides he wants to steal my spellbook, he takes a pretty-but-blank spellbook thats easy to get to, while my actual spellbooks are harder to reach. If he does manage to get one of my actual spellbooks it'll only be 50 pages worth of spells and not my whole arsenal.
In our games we go into quite a lot of detail about how we keep our property safe from bandits.
But to answer the OP's question, yes, it seems foolish considering the number of times it's referenced in the rulebooks that a wizard would only have one spellbook, particularly when the rules have a section specifically on the cost of making a duplicate of your own spellbook. Seems like a done deal at that point.
Have to agree. That gm needs a good sharp whack upside the head with a wizard's second spell book to knock some sense into him.