We're talking about the combat ships that you would specifically take that skill to benefit though? Like I can't imagine taking auxiliary support and then using a bunch of civilian military ships without trying to buff them with the skill. The skill also sucks too, you have to burn so many OP just to get the benefits of the skill, and most civilian ships don't have a ton of OP to begin with. The whole idea behind the skill doesn't really work IMO.
To the contrary, no. You take the skill to generally benefit either a single large vessel like an Atlas II/Venture, or a few smaller vessels like Kites. Whatever you use it for precludes ever using ANY other militarized vessel in your fleet. As-is, the skill does work, it just has a very specialist-focused offering: Making a very, very small portion of your fleet more powerful. In a sense, it's akin to running Automated Ships - you do it with a very specific strategy in mind around a large vessel or a few smaller ones.
When you suddenly make the hullmod a 'default', you run into an issue currently limited (in vanilla) to the fleet carrier skills: You suddenly don't want extra militarized vessels in your fleet, only very specific vessels. In the case of the carrier skills this applies to fighter bays, with logistic/support vessels like the Gemini or Colossus Mk. III suddenly becoming worse-than-worthless trash just by existence of their fighter bays nerfing your combat carriers.
As-is, when using the skill you burn less OP on average than SO for a significant overall boost to the performance of the very specific ship you want boosted. This can turn an Atlas II into a respectable kinetic-focused artillery platform, or a Venture into a Capital-grade armour tank. I haven't experimented closely enough with the smaller vanilla vessels to get a feel for Auxiliary Support builds for them, but neither of the two I mentioned run into any OP problems using Auxiliary Support.