I have revision 2 of the plans and they tell you to machine countersink all the skin holes in the longerons except for the gap cover holes (Page 10-16, step 1). This would include the forward-most hole, in common with the F-1006 bulkhead. Step 3 has you dimple all the holes in the skins with a number of exceptions, including the F-1006 common holes. This is a confusion which may have been fixed in later versions but can be approached in two ways, whichever suit you.
The first is to go ahead and dimple the skin to match the longeron and dimple the corresponding skins to match later in sections 32 (joining the tailcone) and 43 (installing the cabin top - along with the top skin). This is probably the most natural thing to do.
The second is to neither countersink the longeron at this location or dimple the skin. If you read section 32, the forward longeron near this location is not countersunk. Instead, the forward sides and top skin are countersunk for rivets, and you could employ the same technique for the holes where the aft longeron meets the F1006. A variation, for people who riveted the aft skins before discovering the problem, is to countersink the aft skin and dimple the forward and top skins to fit over it.
Either method should be fine. The top skin, which is the overlying one, is thick enough for countersinking so there is no strength issue. I think dimpling looks more natural as the rest of that line is dimpled, but it's not going to be really visible on a finished airplane. Your choice.