Standard engines ARE better than XLs in the most important way: they're less likely to stop working when a side torso is torn off.
That is an advantage but that doesn't make them overall superior. The larger engine allows for more armor or higher speeds which helps avoid side torso losses in the first place. Which is a big reason why people upgrade SFE designs with XLE designs when industry permits despite the side torso vulnerability and C-Bill hike.
That argument also doesn't apply to the XL Gyro which has its extra bulk in the center torso. But any crits on the center torso are most likely either going to hit the gyro or the engine anyways, so that's a wash.
Standard Autocannons and structure are better because far more factories can make them.
If they were better, we'd see a lot more upgrades transitioning from advanced ACs and structures to the standard variety.
I'm not denying that manufacturability is an advantage, but there's much more to it than that. For instance, Rifle Cannons can be manufactured by even more industries than the Autocannons, but they're not better, as they're mostly obsolete in the 31st century battlefield as a weapon system. The claim to fame of the standard Autocannon is basically "It's useful enough that it's not completely dead weight on the field at this time while it's simple enough that we can build it just about anywhere". Which is why it's standard, as opposed to any intrinsic superiority over other autocannons.
Regular ACs are still obsolescent and are poised to be phased out by advanced autocannons when the technology and manufacturing base/supply chain catches up; note how the Clans don't use "standard" autocannons anymore, or lasers or PPCs for that matter.
The problem you point out with so-called "anti-ballistic" armor sounds like a problem with that particular armor, not Standard.
Yes. That's the point.