It's my opinion that this is the result of rig mismatch.
I doubt that "mismatch" is the right term here. You're right insofar that adjustments of the amp/pedals as well as on tone and volume controls might optimize tone on the stock DGT. That way, you most probably will get the best out of it. I, however, couldn't do it, even after playing that guitar as my main ride for almost a year.
My requirement is that a guitar should sound "right" to me (with all pots on ten) when I plug it into my rig that is set to take also other guitars (mainly Stratocasters, that is, but also my Hollowbody II). The DGT pickups were not able to deliver that, especially with clean or slightly crunchy amp settings. With the volume turned back, the DGT quickly sounded thin to me when plugged into such a clean rig.
A Fender Princeton Reverb was particularly happy to unmask the (at least for me) annoying habits of the DGT pickups.
But also my Orange Thunderverb 50 only leveled out the stinging upper frequencies and lacking bass definition when set to Classic Rock overdriven tones. When set to the sweet spot, just breaking up, it got a bit annoying again with the DGT.
Both amps work well with my Strats, my HBII and even my 408MT (that will leave me soon, sadly having a Pattern Thin neck).
If you're working mainly or only with a DGT and really go into detail when setting up your rig, you will probably get your tone (at least David does) sooner or later. But that will mean that you have to be extra careful to always find the right position for the DGTs volume and tone pots (and keeping them set to this position in the heat of battle). For a pro that might be OK. For me, it's not.
I think that the DGT pickups are just that: David Grissoms pickups.
But that doesn't mean that they will suit everybody else (even if given some time to get accustomed to them)...
But again: the DGT is a great guitar, and for me it's no sacrilege to switch the pups to something that suits ME better.
That way, I got the best of this guitar and I don't repent a second that I have bought it.
I personally would always chose a DGT again over a McCarty, as the neck and controls of the DGT are just to my taste.
And those things cannot be as easily changed as a set of pickups and potentiometers...