The thing is that the gain knob do affect any line level instrument plugged in (I've tried an Yamaha Clavinova Electric Piano). The first 8 channels do not give a very convincing response to line level instrument as they are not very loud if the gain knob is turned down. However, there are 4 stereo inputs (channels 9 to 16) that give a better response to line level instruments but you can just control them by pairs on the mixer. I was just wondering if I ran my mics in another preamp then into the mixer (using line level connections (TRS)) with the gain knob closed, if it would be bypassing those built-in preamps.
The gain control works for the preamp AND the line-in. Line signals are much hotter than mic signals, if you run a line level signal into your xlr pres, you could very easily blow em. Just plug your line stuff into the line ins and adjust the gain accordingly. There's nothing wrong with cranking the gain up on a line signal. If you can't make it high enough, turn the volume up on the keyboard. In any case, I'd HIGHLY advise against plugging a line level signal into your mixer's pres. You'd have to run a very quiet signal from the source, and you'd be boosting the noise floor twice! It'd be a VERY noisy signal, it's just a bad idea on a lot of levels..
The stereo channels may have a +4/-10 switch or something, which is kind of a gain adjustment. If you prefer to use those channels instead, go for it. Save the channels with the gain controls for a time where you actually need to adjust gain!
Also, not to be nitpicky, but your mixer takes TS, not TSR for line ins. TS=mono, standard instrument cable. TRS=stereo, like a headphone jack.
The signals are simply different strengths, you have to deal with them accordingly.. Like a garden hose vs a fire hose. Sure, you COULD water your flowers with the firehose, the valve will be too sensitive to use in a practical manner. And you better not open that valve a smidge too much!