It's probably cause Bomberman the AT is significantly different from Bomberman the Costume. Not just in polished models, but the movesets and animations differ enough.
A properly playable Bomberman has a lot more Bomb moves, etc. that it has more similarities to the AT.
It's also possible they don't "care" about the concept and wouldn't disable them anyway. We'd have to see it happen. We have enough precedence to know they could disable the AT, but the closest situation is that they don't with a playable costume, which is almost a playable character in context. Basically it could go either way with no evidence making it clear only one way is possible. When they disable an AT, it's based upon stage logic with the fighters. Moon and Alucard are good examples of this. It wouldn't really mean a thing for Knuckles despite his appearance on Green Hill Zone, and it's easier than doing extra work to make, say, Mecha Knuckles appear in his place. Disabling it is a lot less code.
(Also, to clarify what I mean by wasted development time; to replace an AT, you have to take a model and give it new animations, even if it's just reworking an old one. Remember how Echoes are easy? They aren't that easy. This is nearly the same concept, just overall less work. You have to take the Springtron model, and rig it to do every animation, also program the same damage, knockback, etc. and make sure no parts start glitching. If you want a good example of this, Meta Ridley's costume alone, which is the equivalent of this situation, was buggy till the game's release, due to extra parts. This is what changing a model is for an already used in-game model. You have to playtest it a lot to make sure nothing wrong happens. This in itself is a waste of time compared to disabling the AT. Making an AT playable is a completely different factor is it doesn't remove the AT in any way. A new game that does this of course is a different story. That character wasn't chosen to be an AT at the time, so they didn't sink any time into it, even if the time is just taking data and reusing it, while fixing up the model for the latest system, any bugtesting, etc. And that takes longer than disabling an AT under a specific circumstance anyway.
This is why I could see Springtron appear as an AT in the next game, if Spring Man was playable. I'd apply the same logic even if Spring Man was CP6. It's just plain easier on the development team. Now, keep in mind them making a new character is a ton of work by design anyway. Using an AT model to somewhat help it along is logical, since it has some animations to work with already. Sakurai definitely isn't going to say no cause "it's an AT". Yes, they had work put into them. Yes, they were chosen outright to represent the character cause playable didn't work. However, this wouldn't do anything to waste or hurt development time to make a second version of the character. That, and he did this already in 4 with Conductor Link, an alternate version of Toon Link who only shows up while no Link is playable. In other words, to him, some kind of NPC role doesn't really affect choices alone, since it's far more than that. For instance, say Bomberman was considered for DLC. Sakurai would have to still figure out a plausible moveset in his head, and get permission from Konami. He may be a Mii Costume as a compromise cause he couldn't figure out a moveset he's satisfied with, but still wanted to throw fans a bone. That's also part of why Mii Costumes exist too. Having a good model also helped, since it's clear the Bomberman AT and Mii Costume are a similar model).
I hope I explained that well enough. I feel like I somewhat lost a point along the way too. XD