It has nothing to do with balance. It has to do with satisfying gameplay loops.
You don't get a good customization loop by allowing your players to just slap everything they want on. You restrict things in such a way that it's difficult, or that it drives the need to upgrade/alter slots, or even have multiple copies of a warframe/pet, etc for different reasons.
I mean, you're also running garbage like bite and maul... companions do an insignificant amount of damage, they're essentially there as utility and you're treating yours like it's a secondary weapon.
So now, you have been driven to educate yourself on why all these points are used up and you can't fit anything else... you're engaging with the system more, and that's the measure of success they want. More interaction means more time spent in game, more time in game means more chances to get frustrated and spend real money on plat, etc.
As you get frustrated, you'll move things around and figure out a better combination that suits you, and that ends up feeling rewarding in the end.