The power buildup in the MC is ~400, so 100mW of incident power would give about 40W circulating in the mode cleaner.
Rana points out that the ATF had a 35W beam running around the table in air, with a much smaller spot size than our MC has, so 40W should be totally fine in terms of coating damage.
I have therefore increased the power into the vacuum envelope to ~75mW. The MC REFL PD should be totally fine up to ~100mW, so 75mW is plenty low. The MC transmission is now a little over 1000 counts. I have changed the low power mcup script to not bring the VCO gain all the way up to 31dB anymore. Now it seems happy with a VCO gain of 15dB (which is the same as normal power).