So I am putting the pet's dodge/deflect amounts in their character files directly for now, I will have to keep an eye on otherskills that might not be working as I intended going forward.
You shouldn't do that unless you're really sure it works. The manual in ...\Titan Quest Anniversary Edition\Toolset\guide\database\dbr_monsters.md.html states that
"characterDodgePercent / DeflectProjectile
Chance to dodge melee or projectile attacks (up to a cap of 80%).
Usually granted by skills or items.
Likely bugged if entered as inherent ability. Use these passive skills like instead:
records\skills\monster skills\defense\dodge_1%perlevelx100.dbr
records\skills\monster skills\defense\dodgeprojectile_1%perlevelx100.dbr"
Same for
"characterOffensive/DefensiveAbility
These may be bugged. → Use Dexterity to adjust a character's combat skill.
Also increases via difficulty bonuses."
If they didn't even care to fix the engine, it may not work.
Maybe +2 all skills can do this kind of weird stuff as it also increases item skills. I don't see how +X to Hunting would affect the pet though, as the skill is not in the mastery tree.
My theory is that the tooltip bugs out and displays double the bonus instead of just the bonus (so it would take +2 to all skills and display as if +4....). A general way to put it is if you have skill Level X (as a base) with +Y bonus to skill, it will display X+2Y level in the skill tooltip, instead of X+Y. I've seen that on Bolt Traps default attack skill. I'm not sure if it's only a UI bug or also the game calculates that way.
You'd need to expand the skill levels over very large windows (at least 100 or even 1000) so that + skills don't really matter.
One of the biggest offenders is the pet scaling skill. In vanilla it has up to two levels (lvl 0 in Normal, 1=Epic, 2= Leg), so you may easily end up with Legendary levels in Epic. I've put two separate skills of maximum level 1.