Hi Aleks,
common problems with flashing SPI chips in-system (in-system = without desoldering the chip) are power supply and signal integrity.
power supply => either your power supply at all isn't sufficient or the spi chip draws too quick power that an additional capacitor (of the correct size) closer to the chip is required.
signal integrity => improve your cables, shielding, reduce EMI or desolder the chip and put it on a seperate board, etc.. Or reduce the spi speed, what you already did. Maybe use a different spi clip or solder cables on top of your spi chip if you want to stay in-system.
in-system flashs are always special and depend on the PCB of your target board. some boards aren't possible to flash at all. But I think thinkpads are possible to flash in-system, but it has a low possibility of bricking it.
For sure we have bugs in flashrom. But usually it's power of signal integrity ;). If it's an bug within flashrom, I would also desolder the chip and solder it to a small debug board. So you could reduce other failures soures and to test flashrom in a "known" environment.
Best, lynxis