Ancient and Wise is a result from the Machine Spirit Oddities Table that grants a +10 to all Manoeuvre Actions but also specifically includes out of combat and ramming. Is there any functional difference to simply granting the ship +10 to Manoeuvrability? Manoeuvrability is already a bonus applied in such Tests, and I'd rather just have one bonus to note and keep track of in this case since it looks like both of them apply to all the same tests.

The way manoeuvre tests are written, (test base difficulty) + pilot (spacecraft) + manoeuvrability, may mean that that manoeuvrability is not a modifier, therefore does not count against the +/-60 limit, where a +10 to manouvre actions would. Not that I can think of many other things that add. The only other time it may be important is if something uses manoeuvrablility bonus (as in the way that starship initiative uses detection bonus).

Generally I don't see it mattering too much.

What's the difference?

One would be restricted by the +60 max combined modifier you can apply to a test, and the other wouldn't (as one is a modifier to a test, and the other would add directly to the Manoeuvre stat).