I have a task, remove all modifications directly to the buddypress plugin, I started by replacing bp-default, with a new fresh downloaded copy, and the site stopped working.
Clearly, the site was dependent on something in that dir
So my question is:
Is modifying the bp-default dir consider acceptable?
Its suggested, and is a good practice to not modify anything inside the bp-default theme. So as of your question, 'no its not considered acceptable'. That is because a future update of buddypress will replace everything you've changed. So its better to create your own child theme and do all the editing there.