There is the big one - OEMs have to meet mandated emissions regulations and governments check (see VW). Aftermarket legally has to meet the same regulations, but in practice (at least so far) they mostly have not been checked, and if they are checked it is only after they have sold something and got it installed on a car, while OEMs get checked before they sell anything. Which is to say aftermarket is generally just trading power/fuel efficiency (often both) for worse emissions.
Look at Holley aka Dinan aka APR. They are a publicly traded tuning company. The aftermarket tuning they offer meets emissions standards while still offering better performance than OEM. So yes they are not "legally" required, they still do it to meet state and national laws and to avoid toe stepping.
Yes the little guy tuners don't really care about NOX emissions guidelines mostly because they have no way of measuring the difference their tunes may produce. At the end of the day most OE emissions systems will catch these emissions, and pretty much all aftermarket tuners do not endorse removing emissions systems. to say a tune, or aftermarket parts result in worse emissions is not really the truth. to say the end user removing their cats or emissions systems results in worse emissions is true.
A few years ago all the chip your truck billboards I saw were about removing the EGR value for more power, so they for sure were endorsing removing emissions systems. Though this was about diesel engines and I understand the EPA cracked down on those hard a few years ago. Perhaps the only tuners left put some effort into emissions.
Absolutely, in the past some tuning companies had no issue recommending removing emissions equipment, but then standards and laws changed and most if not all companies complied. Banks power is a good example of a diesel tuner who does not advise on removing EGRs.
In the area of emissions management aftermarkets have found symbiosis. Not only has there become aftermarket manufactures of higher performing both in emissions and performance catalytic converters (G-Sport by GESi). But alot of tuners acknowledge that engine performance can be improved with a well catalyzed exhaust system.
