Recently, I experimented with disabling the bypass valve to avoid the 0-5 psi oscillation. It worked, but as you found, it set off a fault code for the upstream MAP. It looks like the upstream MAP sees a min value of about 50 mbar lower pressure with the bypass tied than with it operating in the normal manner.

Thinking about how short the distance is between the bypass valve and the vacuum source that operates it, I tried a different experiment today. I capped off the bypass valve's vacuum nipple. Then, I put in another Tee where I had tapped into the FPR's vacuum line for my boost gauge. I ran a vacuum line from that tee to the bypass valve.

So, now, instead of seeing the same type of vacuum as the upstream MAP, the bypass valve diaphragm now sees the pressure as seen by the downstream MAP. The result is remarkably similar to tying the bypass valve shut. No oscillation at all in the 0-5 psi range. I didn't notice any elsewhere either. I plan to install a check valve to prevent the bypass diaphragm from seeing boost.

I'll do some testing/logging to see how this works out, but for now, in 5 minutes time, the oscillation is definitely gone, the bypass is definitely open at idle, and less than $5 is missing from my wallet (Tee, vacuum cap, hose).