A Wizard with hundreds of spells in their spell book cannot cast more than any other Wizard of the same level. Two Wizards of equal level prepare the same number of spells and can cast the same number of spell slots.
The Wizard with the large repertoire has more options and can fine-tune their selections if they know what they are going to face. Most adventurers don't have that much insight into what they are going to face so the advantage may be marginal.
On the other hand, a large repertoire can be a boon if they have the time, resources, and inclination to prepare scrolls ahead of adventures.
No you cannot transfer spells prepared as a Cleric into your spellbook
Just above the text that you reference, the sidebar in the PHB explains
When you find a wizard spell of 1st level or higher, you can add it to your spellbook if it is of a level for which you have spell slots and if you can spare
the time to decipher and copy it.
The fact that the book explicitly says that it contains wizard spells is the killer here. Spells that you prepare as a cleric are not wizard spells. They are cleric spells, even if they are on the same spell list.
We know this because of the rules for multiclass spellcasters (PHB pg. 164)
Each spell you know and prepare is associated with one of your classes, and you use the spellcasting ability of that class when you cast the spell. Similarly, a spellcasting focus, such as a holy symbol, can be used only for the spells from the class associated with that focus.
From this, we establish that your prepared spells as a cleric are "Cleric Spells" in that they are prepared as a cleric, and cast as a cleric; not as a wizard. And your prepared spells from your spellbook are "wizard spells" for a similar reason. Even if the two appear on the same spell list, each spell you have prepared is associated only with one of your classes.
The PHB then goes onto explain that when copying spells from spellbook to spellbook:
This is just like copying a new spell into your spellbook, but faster and easier, since you understand your own notation and already know how to cast the spell.
If copying from book to book is the same as adding new spells except faster, then we know that you can only transfer over wizard spells since you can only copy new wizard spells into the spellbook.
Finally, As you have pointed out:
you can use the same procedure to transcribe the spells that you have prepared into a new spellbook
The procedure in question is the same as copying over a new spell, or a spell from one book to another. Both of these processes require wizard spells to work. Thus, even though copying a spell down from memory doesn't specifically add any new restriction, it doesn't explicitly lift the general limitation on the procedure; the precondition that the spell in question is a wizard spell.
Best Answer
Yes, the feature applies to all spellbooks you own. The game rules don't distinguish between main and backup spellbooks, so they are all your spellbooks.