Fortunately, that's why the Applied Skill Handbooks exist, so Tamers aren't forced into using the larger late-game Pals

Why is no one talking about how attractive Angie looks in this outfit?

The tiny chef's hat really sells that last panel.

There's a useful mod for that called AntiPhat, it can optionally resize pals in your party, in your base, in the wild, and in raids, based on their size categories.