There is certainly logic that 'always in effect' is the only non-optional rule. GM discretion can also be 'always in effect but adjudication varies.' Optional Rules are 'always' cases such as caps on armor options. GM discretion are always in effect but at the discretion of the GM. For instance when a medkit runs out of supplies is now a GM discretion item.
You may interpret it how you like for your home game. I'm asking how Bull wants it to work in official SRM games.
Here are several SRM4A references to GM discretion and the effect of not allowing the GM discretion. Many are trivial, some less so.
p147, cannot use Perception without a simple action
p165, fire damage cannot start secondary fires
p168, vehicle test glitches have no 'glitch' effect
p182, can only learn spells from formulas or the exact same tradition - no compatible traditions
p211, magic fingers requires no test for 'simple actions'
p225, no bonus for coordinating in AR
p236, hacking glitches results have no 'glitch' effect
p256, sleeping at all once every 24 hours prevents sleep deprivation
p256, substance abuse doesn't cause addiction
p270, specializations cannot be changed by purchasing a different specialization
p296, critters using innate spell use only willpower for drain
p324, gas and smoke grenades always last 4 turns
p329, walls and obstacles do not block jamming
p337, medkits wont run out of supplies
p342, fingertip compartments may not hold anything
And if they are deemed Optional, no problem, but I don't see your interpretation because the option to ALWAYS treat something one way being banned is a lot different than up to the GM.
That said, all players should assume the GM will give the harshest result of anything listed GM Discretion unless the GM happens to differ. I'm not saying GM discretion is a lever to give players - its merely a variable for the GM that is always allowed in by the book games and thus not Optional. Cousins, but not siblings.