Alright, so I have a few more days of research, support, and investigation under my belt. Below are my updated findings. I am still working with support as well, but no breakthroughs yet.
Regarding non-Meta cables with "power injector" technology, I have discovered that the INIU cable that I frequently use has its own internal "battery management" logic built in. When the headset is charged enough, this cable uses this battery management to lower the charge voltage, which helps the battery charge and remain healthy (great option if you dont need PCVR), but the headset sees this as an issue due to the power dropping (same thing would happen if water/metal shorted two of the pins). Meta added logic to detect this "short" in software V62/V63, and I believe its added to actually protect against overheated ports on the headset that lead to fire and user harm. So although this doesn't actually require a short to occur to get this popup, it also works in a real case, and covers Meta in case of a lawsuit, so they will never remove this popup. Its too valuable for them to sacrifice poor device handling and people using bad cables just for the few PCVR players that are having issues.
So those "smart charging" or power injecting cables will NOT work if they have this smart charging built in. So either a dumb cable with power injecting (i dont think these exist) or a direct connection to a USB C port on the PC/MOBO directly. I do not believe there is going to be a solution to this issue when using the INIU cable, the charging capabilities and the Quest 3 sensing algorithms do not mix well.
Since I do not have USB C ports on my PC, I have been using a USB C to A converter, but USB A doesn't have the same charging capabilities as USB C does (even if its converted right after the MOBO, USB A voltages are 3.3 or 5V only, USB C can utilize 9V, 12V and 20V charging). First thing I need is to add USB C ports, which I will be doing tomorrow, though the board I am installing has a separate power connector to the PSU so it can push more than 5V if a PD device is detected. I will test this with and without the PD capabilities of the board to see how it works, using the Meta cable.