I can be wrong, but seems as hardware mod can be avoided if armbian adds this fixes to the DTS and clk-gpio.c for our board:
https://lore.kernel.org/all/20240906082511.2963890-6-heiko@sntech.de/
Seems as board has proper clock for SRIS mode to work, but it should be enabled on boot. And because PCIe3.0 is split between two devices kernel starts it only for M2 slot, so if M2 slot is initialized before SATA controller it will work, if SATA controller is initialized before M2 it will not get clock signal and will hang. I checked current DTS in armbian and it doesn't have this clock logic.
When we remove a resistor it simply avoids this bug and SATA controller works in a different mode (which could be slower).