Sorry about the wait, I've been a bit preoccupied the last couple of weeks and replies haven't been giving notifications
1. When a player loyal to the USCM (marine, civvie, friendly survivor, etc) bent on disrupting the round or usurping the legitimate command structure cannot be subdued with non lethal force, I think I'd most likely get reported for a BE during a non emergency when there are no MPs or staff officers to deputize, single handedly enforcing the law is difficult (I've done it multiple times across MP CMP and SO) and expecting a CO to reasonably lead the ground and deal with LRP bullshit may lead someone to think I made a bad call in a stressful situation, hence the report.
2.
a. I would likely prioritize the fob squad, if they are in desperate need for metal and cades, no amount of replacement limbs and medicine would save the operation, and if a marine missing limbs is in medbay custody, it is a non priority, as long as there isn't a security risk on the ship, which the MPs can deal with anyways.
b. I would reprimand the PO for taking the law into their own hands violently, and tell the MPs to investigate if the MT in question had taken the powerloader. I wouldn't charge the MT with theft if they had, as it's perfectly reasonable for an mt to take the powerloader if they have a reason to (fixing up the drop ships, loading OB, transporting req supplies, or just getting familiarized with it) but if the CE or PO had ordered them to not take it previously, that would justify an insub charge.
c. I would have the CMP issue a full forensic search of my office, I would personally talk to the staff officer in question, I would tell the CL that they are not allowed in my office without my permission, SO or not. If it was found that the SO did do this (or they admitted to it) I would charge them with illegal confinement, minimum time 30 minutes, if they had intentionally done it to get the CL arrested, or they had caused problems already in the round, or had commited any other crimes during this incident, I would consider giving them the maximum time of permabrig. I would thank the XO for bringing this issue to my attention.