I just did a risk exploration. Fighting the boss I needed to use the facilities/bathroom/toilet/watercloset about 15m in. After 45m I had no idea how much further and the discomfort had increased enough that I decided to screw it and closed the game client.

I had no idea how much further I needed to go. I also had no way to pause the fight because of RL. If you're the only player in a single team map it should be viable to Pause the game. At least some type of boss health bar so I know if I am at 53% boss health or 3% boss health.

I believe that you can just use a Telepipe (purchasable for 200 meseta from the NPC shop) even in the boss room if you need a break; doing this shouldn't reset the boss, and even has the benefit of resetting your Half-Doll usage.

I'll go double check to make sure that they do work there.

EDIT: Looks like Telepipe usage is disabled in the boss room.

The only option is to let yourself die to go back to the Gateway Ship; this doesn't end up resetting the boss, and the only penalty is a lower rank.