Hi, welcome to the forum.
I'm not sure I can help too much, no experience of SD59, but I do have riff raffs in a gibson explorer - absolutely love them there.
My explorer is very dark and woody sounding. It came with the gibson ceramic jobbies (I think they're both 500T), which I quite liked, but I wanted to try the riff raffs I had - I'm more into "vintage" tones. They're lower output than the gibson pups were, so the "wood" is doing more of the talking, as it were. And yes, because of this, the neck is much warmer and darker than it was. But "muddy", I wouldn't call it that on mine, (but others might!) - having said that, I always tend to use a neck pup for other things than 5th chord rhythms, that's what I use the bridge for.
I do suspect you might be getting "more" of your guitar's own characteristic sound with the riff raffs (although with a name like SD59, I assume these were vintage type pups too, with a roughly similar sort of output?)
As far as I'm aware, if the tech was just swapping the pups, there isn't much he could do to make the pup sound bassier without changing other stuff as well - I assume you've got the standard two volumes and one tone, no other extra circuitry that might have confused matters?
I am wondering about the tone control as well though - there's a fair few on this forum who don't use or believe in tone controls, I'm not one of them, I do love tone controls, but I must admit that with the explorer I can't use it as much, it's pretty much set on 9-10. I have been wondering about experimenting with different pot and capacitor values, but right at the moment it's firmly in the "if ain't broke... don't fix it" category for me!