I don't think that Flash Builder has been tested when linked to myEclipse, so you'd probably be a lot safer either running it with its own dedicated copy of eclipse 3.6, or else linked to a full copy of eclipse 3.6.x downloaded from eclipse.org.
If you feel adventurous and want to try it out though, let us know if it works to your liking. Just be sure to make a good backup first, in case you aren't happy with the results, so you can revert easily.
The FB 4.5 Plug-in utility just installs a link file pointing to its base installation, so it's usually pretty non-intrusive, and easy to uninstall if you want to experiment with it. Still, better safe than sorry.
Thank you for the quick answer.
The myEclipse thing will be our bet
Now, forgetting the myEclipse for a moment and just thinking about plain Eclipse.
The other part of the question was if the plugin version (used with a fresh 3.6.x Eclipse) has ALL the functions of the Standalone FlashBuilder installation.
Because we don't want to use Eclipse with the plugin, if we miss some key things like (who knows...) testing/deploying/debugging features...
To my knowledge, the feature set is identical between the two, because when you run from your own copy of eclipse, its linked to the full FB 4.5 installation on disk.