The Germans were anal retentive about re-designating and re-naming even the slightest variation. The Bf109F-2 used a DB601N, hence I doubt there were any changes to the engine itself. As you say, I too think the supercharger was slightly different but that's kind of considered separate from the engine as far as designations go. That would explain minor differences in FTH and whatnot. If they'd changed it there would be a new designation for that engine, which no references to date have ever mentioned.
DB601s did have a chronic production problem, but keep in mind a lot of this was from early 1940. By the time the BOB was over there were more and more 601Ns being moved away from Bf110 gruppen and pushed into 109s. In late 1940 even then emphasis was being given to early 109F prototypes but Luftwaffe commanders were demanding the engine for 109Es and they got their way. Even some 110s that were intended to get the 601N were finished with 601A or Aa and the N engines were diverted to 109E production instead.
In January 1941, just after BOB, there were 112 Bf109s with 601Ns and 135 bf110s with them. The 110s were being built with these engines to replace losses in the gruppen using them, only. They were just there to maintain numbers. This was early 1941, and the number would only shift more and more to the Bf109 side of the scale.
The way I understood it is the E-7 was directly based on the E-4/N. The E-4 had the /N designator to denote DB601N engine installed, but the E-7 didn't need this as the 601N was the default. Now, this could be wrong but from reading up on a large number of BBS discussions on this and half a dozen other forums (often with most insightful quotations or references) I came to the conclussion[ed: a couple years back] that the E-7s had more 601Ns that you would think.
The thing of it is even E-3s were updated to E-7 standards, sometimes including engine replacements with 601N engines. Most still had their 601A engines, but were now E-7s. E-4s underwent the same upgradesand became E-7s. Much like how early E-3s were refitted to become identical to E-4s. After 1940 all remaining Bf109E-1s through E-4s began being converted to E-7s. Naturally there weren't enough 601N engines to replace them all, but the records indicate that even in training schools E-7s became the primary ride. It was a systematic change to upgrade all Emils across the board.
There are cases of the same werk number Bf109E-1 being upgraded and listed as E-4 then upgraded and later listed as E-7. You can even see some photos with the Mg17 wing ports plated over with metal plugs (some even look fabric covered) next to the MG/FF barrels. And yet, these are all E-7s but quite possibly retain their 601A engines.
These upgraded planes also skew the number of 601As found on E-7s at the time they were removed from service. Something like 2/3 of all E-7s had DB601As when removed from duty in 1942, but knowing all the previous versions converted and the slow production for 601N engines and the need to replace worn engines in the field with whatever is available, these numbers can be misleading. At the time they were still front-line fighters through 1941, they were becoming the definite version of Bf109 on the Western Front.
To me, THAT is the definitive E-7 variant and that is what we ought to have included in AH. It would also remove redundancies with our E-4 because if modeled with the 601A it would be very redundant.