I'm confused here…
What exactly about "otherwise works great" do you think needs fixing?
I recall the old saying: If it ain't broke, don't fix it!
Booting through a black screen (you get a white Apple and white progress bar) is the new normal - since 10.10.4 and later. I'm not sure if all Macs got the firmware update to provide that change.
Ah, OK... that works, too...
There's really no problem with plugging in your video cable while power is on, unless that makes you nervous.
If it used to work differently for you, the it could be something that will be fixed when El Cap is released. Or, you should report it as a bug.
Have you tried a different cable?