Obvious but important caveat first: It is your sim, and that sim is your world, so you do things however you please. I will not give you advice on what you should do.
But for what its worth, if it is useful to you or to anyone else, what I do and have done for a long time is:
I “play along” with what the sim gives me once, then I evaluate if this actually realistic or just the sim goofing something up - if at that point I decide the sim is goofing up I ignore it.
E.g., if the sim tells me to go around due to traffic, I will. On my second approach, if I can see that there is not actually any traffic and it is just the sim ATC being broken, I ignore it and go ahead and land.
For your example: If I see excessive magneto drop, I will do what you mention, try to burn it off, etc, if the drop is still too high but full throttle RPM is by the book, I ignore the excessive magneto drop and go ahead and take off.
I find that to be the best tradeoff between immersion and realism. In my view, striving for realism while in the sim is the biggest immersion breaker. No real-world pilot has ever thought “is this realistic? what is the most realistic way of doing this? what would a real pilot do?”. Such thoughts should never cross our minds, IMHO. Whatever happens in the sim “is real” and we deal with it as if it was real. The time to think about realism is between sim sessions, not during sim sessions.
But sometimes that approach just does not work - if the sim does not model things like spark plug fouling or magneto problems but it has an issue with excessive mag drop there is no way treating it as if it was real is going to fix that problem. Do I really want to model an incompetent mechanic who is incapable of fixing my magneto problem, no matter how many times I taxi back to the hangar to have it fixed? No, not really. So I suspend my suspended beliefs for a moment, consider that issue a sim issue, and ignore it.
So that is how I deal with such things. You decide what works best for you.