You cannot guarantee stability just by doing a Monte-Carlo analysis, but that analysis can find parameters for which the control loop will be unstable or give you some confidence that the current parameters are less susceptible to become unstable due to some parameters being slightly off.
Another thing to point out is that the phase and gain margin on their own might be deceiving regarding how stable a system is. In Feedback systems, by Astrom and Murray Example 10.8 shows a system with good margins (phase and gain) that is actually close to being unstable, and that can be detected by looking at the Nyquist plot. Overall the book goes over a bunch of interesting concepts, theory- and practice-wise.
Another aspect that they cover is the part on Robust performance (which will give the guarantees to small changes in the parameters of linear systems) and the chapter on Fundamental limits. Having an actual procedure to determine how robust a system is to changes in its parameters might be why you do not see MC being done in the linear case.
Overall, doing MC might be a good starting option to look for parameters that can cause the system to become unstable but will not guarantee, if you don't find any such parameters within the range you looked for, that the system will be stable. While there are mathematical analysis that will give you such guarantees, and even procedures to determine parameters that lead to a robust controller. But the math used for that can be a bit daunting so it is not as popular as some heuristic techniques.