Very hard to do much about it. On the front of the body, you are only going to see the bit behind the bridge, as most will be covered by the scratchplate. But the back will be more visible (though obviously not seen much when playing). That centre section has a definite grain pattern as well, so itself has lighter and darker areas.

I have the same problem on a Gordon Smith Strat I'm refinishing for a friend, and that was an AUD$800 guitar when new, and very badly finished indeed. But that was, and will be again, a sunburst, which reduces the impact of the darker central section.

You could try two stains, a light amber for the centre piece and a darker amber for the lighter sides. It won't work perfectly, but it could reduce the contrast between the two colours to a less noticeable level. You'd need to mask off the areas when staining, but you still might get some bleed between the two stains. Or you just accept it for what it is, and live with the mismatch.

If the darker section was more central, you could almost make a feature of it. You could even consider painting a solid dark stripe down the middle of the guitar, and have the wings amber. Or do a solid butterscotch paint job.

The more expensive GTL models are the best ones to get for doing a straight amber/butterscotch or butterscotch blonde finish on. The basswood bodies TLs always have more variance. Basswood can be quite figured, but it is more often than not very plain, of mixed hue, and best suited for solid colour finishes.