There were several things wrong with this I thought:
1] In fairness knowing Samus was about to go into a hot area/just entered one, it would seem that to be the logical point to give Samus "permission" to use her Varia Suit. Not only realising much later with a boss arrival. Some may consider that tension, I say infuriating.
2] I only found all this out on a whim since I'd explored everywhere else and it seemed stupid to have the only way forward was through a heated environment before getting said suit.
3] She's a Bounty Hunter, a rebel, she can tell the rules to go fuck themselves and activate whatever she wants whenever she wants. Yes, it's a different twist on the losing all powers and having to regain them concept. It was just handled piss poorly.