Spoilers Obviously :P

I'm not sure if this will be helpful.

I noticed that after the second scan with the TOPAZ scanner, and before initiating the third scan there is a safe in the garage adjacent to the scout tower. You can dump your entire inventory here to return after Skif gets knocked out and you obtain the bolt. Meaning, You don't lose anything after the prologue. This is my first time posting something like the hope of assisting speedruns. If it isn't useful I completely understand :]