“It is a truth universally acknowledged that though all rules are optional, some rules are more optional than others.” — Aristotle.
Back in the very early middle Eighties, E. Gary Gygax occasionally published a peevish piece in Dragon magazine in which he animadverted against people playing AD&D wrongly, for example by using THAC0 instead of specifying which line of which combat matrix an NPC or monster attacked as. “If you don’t play by the official rules” he told us “you aren’t playing the Dungeons & Dragons™ game!”. We responded with derisive laughter, and since then no-one has threatened again to send the RPG police around. Since then all rules in all RPGs have been optional. But in practice some are a lot harder to opt out of than others.
At one extreme you have rules that you can simply ignore without that making any difference to anything else in the game. For example the rules in GURPS for a character’s height and weight in feet, inches, and pounds as limited by that character’s ST characteristic and build disadvantages. These only make sense at all if your character is a normal human, and the main point of GURPS is that characters needn’t be, but fortunately you can just turn the page, leave spaces blank on the character sheet, and ignore those rules. Nothing else in the game is affected in any way.
Then you have rules that are properly optional, in that they aren’t completely pointless, but about which you can make a simple clean choice to use the option or not and it will change the game in a way that you might well want or not, that is clearly explained at the point where you choose it and properly carried through all the systems affected in the game’s design. An example of that would be the choice of “Purist” or “Pulp” mode in Trail of Cthulhu, or the combinatoric choices of “Stakes”, “Dust”, and “Mirror” modes in Night’s Black Agents, or the choice between the basic combat system in GURPS Spaceships and the tactical space combat system in GURPS Spaceships 3 Warships and Space Pirates.
Then you have rules that are optional in the sense that they deal with an aspect of play that you might not include in your adventures. The very first paragraph in Chapter 8 of ForeSight (the spaceship construction, operations, and combat rules) is a designer’s note urging you not use them because (i) little roleplaying occurs in space combat, (ii) space combat is too deadly, and (iii) spaceships are too expensive for PCs to own them. That’s all very well for a subject that doesn’t arise in most games, but it is a nonsense for a subject that has a big part in most campaigns in the genre that the game is ostensibly designed for, as for example combat rules in most RPGs.
Finally, you have rules that are optional in the sense that no-one is going to send the boys round if you don’t use them, but that you can’t just switch off without either (a) tracking down and patching a great many references to them and interactions with them scattered throughout the rules, or (b) designing yourself something to replace them. For example, the injury multipliers for different damage types in GURPS are not optional rules except in the trivial sense that every rule in every RPG is optional.