Asides from visual, it can also be the placement of the O2 sensors. I have no idea, nor should i guess, as to cause on enkrypt3d failure but some poorly designed headers have the o2 bung on one of the header pipes instead of at the collector (i'll look to see if the TS headers have this problem but I don't think they do based on memory). The sensor then only collects information from that single cylinder which can potentially have some other underlying issues. OBDII cars are more sensitive to exhaust changes in general but they also probably run cleaner when it's working haha.
Bats - I agree with you that getting the cats up to proper operating temp *might* be the problem in some isolated cases (this is actually the first i've heard of headers failing smog...shrug) but most mass-marketed headers for our cars don't move cat placement relative to stock. I would also agree that NA2 could be the equivalent of "shorties" in the American V8 world. Long tube is ideal to better manage/optimize the exhaust pulses but i'm not an expert on this subject.
Asides from some fitment issues for some folks, the one area the TS headers don't do well is in the collector.
The TS headers look like this:
A more expensive header with a better collector should look like this:
Then you start thinking... well... do I want to spend double and sometimes waaaaay more than double for a few extra (5+hp?) ponies? That's my argument. This is why I don't think the TS headers are "junk" per say. Personally, I'd rather spend it on suspension or non-compliance parts that actually will help me go faster but everyone has different priorities.
Also, if someone is interested in a layman's explanation on short tube vs. long tube headers I found this video to be worthwhile. Start around 6mins:30sec.
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