File system content will be security trimmed based on the file ACLs. The
SharePoint crawler will ignore the share level permissions, since the
content might be accessible through multiple shares.

So if a file's security setting is set for domain group A, a SP user who is not
a member of domain group A but is a member of domain group B will not see the
file (regardless of any SP permissions)?

That's the way I understand it. You mention "SharePoint permissions." SP
permissions on what? You can't put SP permissions on files in a file
share since they aren't in SharePoint. Which sp permissions are you
worried about impacting this?

I guess I was thinking more about a role..such as if the person in
question was either a Site Admin or reader only..
But you are correct..not sure what I meant actually..just covering my bases.

True. As long as the user is not a member of an Active Directory group that
has NTFS permissions to the file itself the user won't see the file no
matter what SP groups they are a part of.

Our biggest issue was finding files out there that had Everyone, Domain Users or
AUTHENTICATED USERS set on the NTFS permissions :( when it should have been more
restrictive.

Users thinking that securing the file share alone is security is also a big
problem.