knowing the nature of sigma.. im sure he would customize his larger body ahead of time to fit.. sigma never comes with the "clothes on his back" so to speak
look at most of the levels he is in.. sigma is always the final boss bastard with a trap like environment set up waiting for X.. everything sigma does is a giant elaborate trap set waiting

even if the arena was too small to fit the large body of sigma.. he would then fill up whatever space is available with his body.. probably made up mostly of sigma's invincible areas
now where would kuja go with sigma filling up all the space? with his enormous gun pointed in for example?
"like shooting fish in a barrel"