Unrelated to the main topic but your data log seems to indicate you are not turning on IBBS and allowing G3X to power up before engine start. Is that true?
My normal practice is to turn on IBBS when I get into the aircraft. G3X is powered up before I have the belts secured. GPS normally has a good fix and AHRS is aligned before I attempt engine start. I don't know that starting immediately after IBBS is turned on causes any problem. I simply prefer to check as much as I can, including all the alerts, before start. It also allows a confidence check of the loaded IBBS voltage and that all systems that should operate on IBBS actually do.
My logs show my GPS acquisition sequence is 3D, 3DDiff, 3D(XPDR), 3DDiff (XPDR). Your log shows only 3D, 3DDiff which indicates the GDU internal GPS is in use all the time and the higher integrity transponder GPS is never used. Don't know if your aircraft GTX/GDU interface is configured differently from mine perhaps because your original build included the GNC. It's something I'd want to understand if it was my aircraft.
More closely related to the original topic - I also noted that your battery charge after engine start peaked at 12 A but a recent log of mine showed peak of 28 A. It could simply mean you battery is in better condition than mine. Was this log with the new battery?
Cruise battery charge current is very similar to mine except for the brief discharge anomaly.
Still think you have an intermittent alternator or an intermittent wiring fault. A problem with the shunt sense wires would not cause the simultaneous drop in main bus voltage.