The line ins have -10 dbV, +4 dbU and a 'low' setting. Those are not really used as gains - they are standard levels expected from 'pro' (+4) or 'consumer' (-10) equipment.

Only with preamps feeding the line inputs you'll have full control. But if you use them for keys or a git DI or whatever no one keeps you from using the most suitable of the three steps. As far as my experience goes it's not a practical problem. If I get levels between -25/-10 db I'm fine as long as I record in 24 bit.

If a signal is too low to get a proper headphone mix while recording it can be boostet with the dynamics section easily.