Hi Trevor,
You have to be careful in this situation, indeed.
# Adding stuff
I have my own bundle where I add all kinds of stuff and try not to change the default bundles. A clever naming theme for those item (I use All: foo, CSS: Insert Color, Text: Footnote, ..) will make it manageable.
# Basic Snippets
I changed all the snippets in the PHP bundle to suit my code formatting. Those snippets won't be updated anyway, because they are very basic. So, no worries about losing new functionality.
# Changing complexer things
I'm listening on the TextMate dev Mailing List for bundle changes (and I'm in the IRC channel most of the time) so I know, what's going on. Also if you check out Bundles via subversion (what you don't seem to do) you can see, which items changed. If I see any interesting stuff there, I will have a look at it, and merge or replace my stuff. Otherwise making a duplicate of the particular command in your own bundle and changing that, brings you some way. Sure, there will be a popup dialog asking you what to execute when triggering the shortcut. Unfortunately, changing a bundle item keyboard shortcut will duplicate the whole thing. So either you make a new shortcut for your own stuff, or live with the dialog. If you are sure, your adapted command is better in some ways, then the default command, be sure to post it here on the list, others might find it interesting too and your version could make it into the default bundle.
# Bundle Editor
There were some proposals for how to improve the Bundle Editor and include a versioning and merging of Default bundles, local changes and SVN checkouts. I had wanted to whip something together (just a command line script which compares dates and makes diffs, to view and make patches), but did not find the time yet.
So. I don't know if that was particularly helpful.
Soryu.