Yes, even under your definition, being arrested for taking meth you make yourself in your own meth lab is an attack on bodily autonomy--you intervened on your body with chemistry rather than physics (self-surgery examples you've given), but how is that relevant?

There are limits to bodily autonomy, but those should be considered very carefully.

Some psychoactive drugs are a reasonable target for these limits because they can impact a person's ability to control how they negatively impact others (same as speed limits).

Other drugs are a reasonable target because they too directly target the body's reward system, overriding the person's effective autonomy to make decisions about it. If we value well-being, not just autonomy, there are exceptions to be made here.

Point is, they should all be carefully considered. The default right should be for autonomy, and only cases with very good reason should be exceptions.