JB Weld is an epoxy. I have West System pump dispensers on cans with both "quick" and "slow" hardeners that I use for various things (I'm a boater) along with their collection of thickeners (various ones from microballoons which produce a reasonably soft surface to what amount to shredded fiberglass which makes something much harder, almost rock-like, when cured.) Epoxy by itself is not particularly structurally sound but when mixed with a thickener, depending on which it is, it certainly can be. In this case you want the mixture completely filling the existing holes and leveled out with the wood, which you have to do before the stuff kicks *and* without getting it where you don't want it. I'd use microballoons for the thickener just so you have some crack at reasonable shaping/leveling once it cures, but you will wind up having to dealing with access to that immediate area. Because it will be harder than the relatively soft wood it will be difficult to work once cured. On the other hand that's the point here, in that you have a structurally-compromised area of the playfield that also takes fairly decent impacts during play due to that target being struck and you certainly don't want it to fracture. You will have to re-drill the screw holes when done using a drill stop so you don't go too far but that's good rather than bad since you can precisely locate them so the target is in the correct place.
Coming up with a way to flip the field and support it is not very difficult; removing the apron should give you plenty of room on the front end. The rear could be a bit trickier and you'll have to pull some of the playfield pieces but supporting it adequately when flipped over isn't that hard to do. The nice thing about Pin2k playfields is that they're designed to be able to be removed very easily and set flat on a floor without damage to anything on the bottom, so doing that while looking at how you're going to flip it over and rest it on something (like a set of sawhorses) isn't difficult.
Make up some of whatever you intend to use for the fill and practice on a scrap piece of plywood that you have laying around if you've not done this before to make sure you like the consistency and hardness of what you intend to use once it cures. IMHO best option is to find someone with the west system two-part components and microballoon thickener. You need very little and buying them at a boat store or on Amazon is going to result in buying an enormous amount (at some cost) for what you need to do. I would not try to use wood filler as that stuff has effectively zero structural strength, and you need some strength here since the target base is screwed to it.
Trying to reseat the big insert is probably going to wind up causing more problems than it fixes on a clear-coated field like this because you will further fracture the bond between the insert and clear. The ghosting will probably get somewhat worse if left alone but I'd be inclined to do exactly that unless you're looking to do a restore -- as opposed to that target that you need to fix.
Occasionally you can find a playfield that's complete and "drop it in" with zero work since SW:E1 and RFM were kissing cousins and they were made for conversion purposes. If you really like the game and one comes around at a rational price in good condition you might contemplate doing that; it also would give you a nice bin of spare bespoke parts for the game going forward......