You have the background noise squelched, which is similar to my Yeasus. So the way it works for me is that in FM or AM mode it stops and pauses. In SSB or CW, it just slows down.
That's because when the radio starts to cross an SSB signal that breaks open the squelch it may not be at the right carrier frequency, so it's giving you time to click the scan stop (PTT on my radio) and center the frequency (which is adjusting YOUR radio's BFO). Remember that FM and AM are set bandwidths with a transmitted carrier, whereas on SSB your radio is re-installing the carrier (remember SSBSC?) and so it has no idea when to stop. You do that with your ear.
FWIW, doing this automatically can be done, but it's a higher level of sophistication to the carrier recovery than is usual in ham radios and starts to become far more difficult when dealing with speech of so many different people, especially so when dealing with interference, static, etc. Turns out that what your ear and brain are awesome at doing (detecting minimum levels of comprehension) takes pretty dang powerful DSP. DSP works a lot better (e.g faster and needing less processing capability) on deterministic and periodic signals, neither of which the human voice really does.
You say after bonding you can't a tell a difference. When I bonded my exhaust in particular it made a huge difference in ignition noise. I still have a lot of alternator whine, but I haven't done much to alleviate it. It could be that your installation location is very good and so was immune to vehicle generated QRM inherently.
'91 Pickup - Imelda
'08 Tacoma TRD - Donna