I thinks it's all a matter of perspective. ID vs. mainstream then no, the ID companies (as a whole) will outperform most , if not all, mainstream companies for a lot less. I'm talking higher dollar subs. I'm guessing the sub $500 category doesn't have much in terms of profit margin, but there still will be difference. I'll give you my experience as an example. Before I heard of AVS or ID companies, I bought a Revel B15a (MSRP $3K). While it is a good sub, for the price I paid for it, I could have bought any other ID sub in that price range that would leave it in the dust.
Now when you compare higher end ID vs. DIY. It's the same story. For slightly more than the the price of one of the premier ID subs I can build two sealed LMS 5400s and LG clone amp. There is no comparison between the two. As good as they are, a single premier sub can't compare to the headroom of two LMS 5400's with sufficient power.
Keep in mind I am referring to the well known ID companies here like HSU, Rythmic, Seaton SVS, Epic, JTR, etc. I'm sure there may be some unknown ID companies that are not much better than the mainstream offerings or worse. In those cases, that could be the reason why they are not well known.