Pretty sure you’re misunderstanding me by a large margin here. I’m not going to purport to be some expert in fixed wing aircraft when most everything I’ve done research on relates to rotary wing applications, but I have come across a lot of ancillary information on a lot of aircraft to which I’ve considered doing projects on. So, with that out of the way:
The F-15E is not just a F-15B/D with bomb racks thrown onto it. It’s got a heavier structure to support that, plus all kinds of equipment related to the strike mission that don’t just come off when you ditch the bombs. In pure absolute terms, that means it’s got a lot of dead weight that doesn’t go away. Is that a huge problem? I dunno; but in terms of performance, it is going to have an impact on how it can fly and fight in the air. A good crew can make all the difference there (and I’m pretty sure the F-15E crews are some of the best in the business) but we’re assuming equal skill levels here. In that instance, an F-15A/C isn’t having to tote around a bunch of extra stuff unnecessary to the mission of air combat. Strictly speaking, the 15A/C has a lot more options than a 15E does; the same is true of a lot of other fighter aircraft of similar generation.
This goes back to my original point which is no matter how badly we may want it to be, you cannot have a warplane that’s exceptional at every single task from strike to interception; there’s just too many special considerations for each mission that would end up in the aircraft being a dog in one mission or another. See the F-111 for that example. This results in compromises, of which the F-15E is one… In that it trades some A2A capability for a very strong A2G capability. The Super Bug is the same way, though it trades far more capability to be able to have a much more varied mission set.
TL;DR A type like the A-6 is always going to have a stronger long-range attack capability than another aircraft not purpose-designed for the mission. You always have to compromise somewhere on something to get the capability you want.