I have not dug into the WP code thoroughly enough to know exactly how it works, but indications seem to be that when WP needs to modify .htaccess, it just "rewrites" it using the "new" rewrite rules, rather than doing any kind of "smart" append or anything.
Things like changing your permalink structure (which rewrites the "rewrite" rules) and, of course, updates to WP seem to be the principle times this happens, though there may be other situations that I have not encountered.
That said, what I have done is just keep my "original/working" WP .htaccess available so that I can easily "merge" it with the "new" version if WP rewrites it. I have not really considered it a problem as it happens infrequently.
(Weird - I originally posted this, in this thread, hours ago at 1754 PST, but in response to another user's (or sock puppet's) post. that is no longer here. I can get to this post's "original". but it doesn't show up anywhere in the "threaded view" though it does show up in the "flat" view and in searches (but not the individual Forum summary screens . If this is a "repeat" for you, I apologize - I just wanted the OP to see the answer so I "re-posted"