ouch. Well the main thing with stock head units and factory line out convertors which we have 1000 threads like yours is again me explaining for the 1000th time on this forum(not your fault, just no one factors in real world factors when doing setups) So stock speakers are pretty low quality. Inside the stock head unit even though you dont have an option to change it, there is a high pass filter built straight into the head unit to protect the shitty factory speakers. So now you have a signal with the bass cut off. Now you are trying to boost that signal with an LOC, what happens is you get an overload of higher frequencies and really cut down low frequencies which explains your clipping at higher frequencies. Also boosting a weak cut off signal like that results in massive clipping and distortion. You should be overall louder across the spectrum but due the signal restraints, you are clipping prematurely before the amp can actually perform properly.
but this is why i ask if you can do the test I outlined earlier because your phone outputs a full range signal.
Everyone underestimates the power of a clean dedicated subwoofer signal from a head unit with a quality dac. You will definitely gain from swapping out a stock head unit with an actual head unit always from all the installs i've done. The head unit is THAT important.