I have a 1999 LS400, wondering if I install an aftermarket head unit,will the Keyless entry still work? - head unit Alpine ILX W670.

 

I don't see why it wouldn't. Hopefully, someone will post a definitive answer.

 

The head unit/nav/amp/etc is completely separate from the MPX system, you'll be fine on that front. Actually wiring it up is a separate story

 

Yes, it is a separate body control module. I (paid a professional) who removed the stock radio on my 98 and have a full standalone head unit, amp, speakers. I have navigation\touchscreen and the only difference is that the audio button, when you press it, just shows a screen that says "audio off" as the radio is no longer in the car. Everything else functions perfectly.