So for bundle items you should change key equivalents
via the bundle editor.
A quick way to find an item and edit it is using Bundles → Select Bundle Item… (⌃⌘T).
Locate the item (e.g. enter “comment”) then press option-return to edit that item.
Doesn't work on my system. I can edit and save the "Source" bundle and then
the shortcut is shown correctly in the "Select Bundle Item" window. But, it does
not work: the shortcut is ignored and I can only comment lines going via the menu bar.
Also the default keyboard shortcut does not work anymore (as expected).
After restarting TextMate, the default shortcut appears again in the Source bundle and
works as if nothing was edited at all.