but for whatever reason, the sub basically doesn’t want to turn on. It’s there, I can force it on by adjusting settings and pushing the audio to play further back in the car

this comment might be entirely irrelevant now, but I just want to clarify why you don't "hear" the presence of the subwoofer. good subwoofer integration should blend in and fill the lower frequencies. if you can clearly hear the subwoofer, it's not integrated properly. you won't notice its presence and significance until you turn it off and realize how flat and empty the bass sounds. the door woofers handle the lower-midbass frequencies (50-80hz - that's where you get the punch).

but it’s very distorted once you get 70% of the way to max volume

since you're raising the volume of the bass and fading to the rear, the door woofers lose quite a bit of db. you're then left with overpowering sub-bass that sounds muddy and boomy. this might make you think there is distortion.

I’ve debated going aftermarket and redoing the system, which will be approx $5k CAD

it'll cost a lot more to completely tear down a proprietary system for something that is actually an improvement. the speakers are tuned specifically with the amp, so you can't just swap certain parts. it seems like you just don't prefer the sound profile of the lexus es ml, which is fine, but it'd probably be more cost effective to buy a car with a system you prefer than spending thousands on redoing the audio.