That'sa exactly what I'm seeing
9/12/15 11:22:16.168 AM WindowServer[191]: CGXMuxAcknowledge: Posting glitchless acknowledge
9/12/15 11:22:16.312 AM WindowServer[191]: Received display connect changed for display 0x4280382
9/12/15 11:22:16.312 AM WindowServer[191]: Found 1 modes for display 0x04280382 [1, 0]
9/12/15 11:22:16.313 AM WindowServer[191]: Received display connect changed for display 0x3f003f
9/12/15 11:22:16.313 AM WindowServer[191]: Found 1 modes for display 0x003f003f [1, 0]
9/12/15 11:22:16.313 AM WindowServer[191]: Received display connect changed for display 0x3f0040
9/12/15 11:22:16.313 AM WindowServer[191]: Found 1 modes for display 0x003f0040 [1, 0]
9/12/15 11:22:16.313 AM WindowServer[191]: Received display connect changed for display 0x3f0041
9/12/15 11:22:16.313 AM WindowServer[191]: Found 1 modes for display 0x003f0041 [1, 0]
9/12/15 11:22:16.315 AM WindowServer[191]: _CGXRemoveWindowFromWindowMovementGroup: window 0xf16 is not attached to window 0xf17
The screen flickering is only just noticible, more just the menubar at the top that flickers - the same level of flickering you see when it switches between graphics cards.
The whole graphics card switching has been a fly in Apple's ointment for a long while - it's been the cause of many hard freezes on some MBPr's - mine included, right to the point that I had the logic board replaced because both Apple and I thought it was needed as part of the replacement program - was excited to get it back thinking no more crashing, alas not the case.
The only way I stopped it was to roll back to 10.9.4 - the bug seemed to appear in 10.9.1, resolved in 10.9.4 and came back with vengeance in 10.10 - seems to be a lot better in 10.11 but nowhere near as good as 10.9.4.