Yeah, every new motor that comes into my possession gets snipped to 3” phase leads, terminated with an mr60. Conformal coated, wires individually covered in nylon braid & fed into grey connector cover.
Currently, until I figure out what connector I want to use, sensor leads stay stock, but doubled/tripled over themselves to preserve wire length but also make ~3”/4”, & kept tidy w/nylon braid or Tesa tape.
Since I use integrated decks (Haya/Rocket Core) I like my leads coming long from the esc to the motor, which stays static length. Always very quick to re-terminate esc leads length if needed…
Also, I like to think it’s more modular than you think - in a pinch, you can just plug lone 3.5mm bullets into an mt/mr60 both ways… if you’re one of those weirdos that re-terminate everything with 4mm bullets, which I’ve deemed completely unnecessary having personally witness some of the most ass-hauling amp pushing users of the form never having an issue arise from 3.5mm’s… that’s yo problem.
If I ever switch over to non integrated decks & have to start using bottom mounted enclosures, I will likely start making use of more convenient panel mounting methods. But still… aside from an ultimate weight saving shortboard, I might stick to snipping motor wires & using a daisy chain from motor connector to panel mount connector 
Introducing more points of failure in your wiring harness makes riding more fun, or something like that. & when none of them ever fail you can circlejerk about your soldering skills.
I’ve also witnessed way too much wasted time from users posting on this forum & irl, trying & struggling to tidy their wiring internally & externally purely because they don’t want to fuck with the stock wire length & re-terminate… I find that weirder than my obsession of stubby motor leads, which take… minutes, at most.
I think after going back & re-reading I kinda misinterpreted what you said - you’re definitely right, but when it comes to phase leads, connectors making use of 3.5mm bullets (mr60/mt60/etc) are plug & play w/individual bullets. So if you do have a panel mounted mr60, need to throw on a new motor last second, your stock motor leads will plug & play for more than long enough. Sensor wires are a different story, but anybody in DIY w/more than one board should have a stash of adapters because every stupid fuckin motor vendor wants to use a different typically anemic connector (looking at you jst-zh 1.5mm pitch or fuckever you’re called) for sensor wires.