I don't think a new thread on the same subject as your other
http://www.vansairforce.com/communit...d.php?t=145712
that so far is at 69 posts, is likely to resolve this for you any more than the other thread did.
But to directly answer your question...
There are a number of places that the plans specify a process that will end in the result you describe.
Another is on the wing spar screw holes where the fuel tank attaches.
In these areas, the enlarged hole is expected.
So the only time you actually need to make a decision on this is when you are going off plans and making your own engineering decisions.
It is entirely possible that in at least some of those cases, answering your questions is not possible because it will depend on a lot of factors (loads, etc.) that can't easily be resolved with a generic yes or no.
Bottom line is the holes in the battery tray were expected to be enlarged slightly.
If you are uncomfortable with that then you need to do some engineering analysis to decide what you are comfortable with. A few questions in a thread here on VAF is probably not going to provide a training course in engineering that can provide you with enough knowledge to properly make that decision.
So what it then comes down to is do you have enough desire to learn that you are willing to read a bunch of books and maybe take some classes, except advice from others here on the forum that may already have the training and experience to make a correct recommendation, or just do the work to make it match the plans......
Your choice.