Using high-level inputs on a powered sub means your signal path to them puts two separate concatenated power amps between source (or pre-amp) and the the speaker driver, while your mains have only one power amp between source and speaker.
While you may not perceive the added delay between the subs and the mains, a purist might argue it's not good practise.
I think the speaker level input on subs (instead of line-level) was there as a convenience for the wiring, but the marketing team decided that could make up some FUD about it being better.
On the other, if you are running long cables carrying line-level signal between amp and sub, you need to not go too cheap on those cables, else you risk a bit of noise pickup. I run 4m or so, from my amp's pre-outs to each sub, with no issues at all. I use the subs' crossover settings knob and volume knob to blend with the small main speakers (with blocked rear ports), but it took me 3 days straight to get the settings right (no suckouts or booms) without using measuring gear (just my ears, a bass sweep tone, and dozens of album tracks; the latter being the best in the end).