@JDW This the double bong problem is so puzzling. Does it reliably continue to happen after the WarpSE is removed unless you wait for a while?
I suggest maybe to test this that you go back to version 0.6b or 0.6a and see if it continues to happen. By the way, 0.6c, 0.6d, 0.6e, and 0.6g are not fully functional so the only versions in the 0.6 series I recommend trying are 0.6a, 0.6b, 0.6f, and 0.6h. 0.6a is similar to the 1.x and 0.5-series versions, 0.6b integrates a new startup sequence, 0.6c, d, and e had revisions to the RAM controller and PDS bridge but were not fully functional. 0.6f is the first version with the RAM and PDS revisions that worked for me and with which I could find no further timing or logic mistakes. 0.6g removed the fixed wait state sound slowdown and made some preparations for the next hardware revisions but had a mistake that caused it not to work on the current hardware. 0.6h fixed that mistake. So in the 0.6 series, I only think 0.6a, 06.b, 0.6f, 0.6h are worth trying.
You also said it did occur at least once on your stock SE motherboard. Is that correct?
Another thing you could investigate is, when the double bong occurs, does the reset signal pulse low? In that case, a chip on the motherboard or WarpSE must be driving it. There are only a two chips in the Mac SE that can drive the reset pin low. It could be the Sony sound chip, since it generates the power-on reset signal, it could be the onboard MC68000 CPU, since it drives reset low when executing the RESET instruction. The BBU and other I/O chips receive the reset signal but I don't think they can drive it.
So if you can get the double bong to happen while monitoring the reset signal with an oscilloscope, then we can see if it's because of the reset pin being pulsed low or because of a software issue.
If the reset pin is pulsed low when the second bong happens, we can temporarily remove chips capable of driving the reset signal. For example, we could take out the motherboard CPU and Sony sound chip. I believe the motherboard CPU and Sony sound chip are unnecessary when using the WarpSE. Of course, without the sound chip, then SE will not produce audio, but the WarpSE duplicates the other function of the Sony chip, which is that it drives the reset pin low until power is ready. Because the WarpSE's CPLD drives reset low for almost 0.3 seconds when it powers on, as long as the power supply is a reliable unit that ramps up quickly, the Sony chip's power-on reset function is not needed. Then the test can be repeated and more chips added/removed until the problem is isolated.
If the reset pin is not being driven low when the second bong occurs, it may be a software issue, perhaps relating to RAM retention.
I have a thought to test for this. Remove two of the four RAM sticks from the Mac SE such that it only has 2 MB of RAM. The WarpSE will be able to operate and will have 4 MB of RAM, although the framebuffer and sound data in the motherboard RAM may be corrupted. This corruption, if it occurs, is harmless and not even "visible" to software running on the WarpSE's CPU. It's just a visual issue and will in no way affect execution. I think moving the mouse over any corrupted spots will cause them to reappear. The underlying problem will be fixed in the next hardware revision so that you do not need any particular RAM quantity in the Mac SE, but for now any visual corruption will have to be ignored if if occurs during this particular test.
Anyway, with only two RAM sticks and the WarpSE installed, once you are able to get the double bong, remove the WarpSE and see if you can get it again. If so, then reinstall the WarpSE, reproduce the double bong, remove the WarpSE, but then switch the RAM sticks for the other two which were not recently used. Make sure to leave the WarpSE out of the system and reboot. Double bong occurs? Try switching back and forth between RAM sticks to see if that affects the ability to get the double bong.