I don't know if it is okay or not but it got me curious so I got out my
old scope and tried to replicate what you are doing only with my Carte
Blanche II card.
I first connected my probe to phase0 pin of the Apple IIgs slot and to
ground on the slot. I then removed my USB connection to the Carte
Blanche II.
Powered up the IIgs and got a wave with some ringing but less than what
I see in your pictures (my scope is an old analog scope).
Turned off the IIgs. No signal on scope.
Plugged in USB. Still no signal on scope.
Tried programming the Carte Blanche II. It won't program without the
IIgs power on and still no signal on scope.
For what it is worth. I leave my USB connected all the time and program
the FPGA or Flash the non-volatile memory over and over without turning
anything on/off.
Is your USB connection to a USB chip on your board or is it a USB to
JTAG cable?
Charlie