It did! Its a rule I've been using in various forms at my table for a while, as I play with a larger group, so when players suddenly lost an entire turn as a result of a couple unfortunate d6s it can be a bit of a bummer.
The "Relentless" rule can be seen as making Structure Checks a bit less punishing, but I've found that losing HP and the effects of System Trauma tend to be impactful enough, and Stuns can be rough for players as it denies them the opportunity to participate in the game. As for side effects, there are none that I would personally view as negative. Its generally let my players be more aggressive and take risks, which leads to exciting moments of combat storytelling, and the slightly increased presence of "System Trauma" instead of Stunned makes it feel more like your mech is being torn apart as you the players fight tooth and nail.
You are indeed correct! You take the normal effects of a structure check, but treat a result of 1 as simply failing to gain the action.