Nope - good question.
I also play electric and acoustic guitar and electric guitar is a totally different animal.
Low-tech, lower output passive pickups through primitive (by bass standards) tube powered gear is usually much better for electric guitar, especially where overdriven tones are concerned.
Overdrive tends to boost the mids & highs, which will sound harsh & brittle and tear your head off unless they are tempered by some speaker inefficiency. This is why those low-watt 25 watt 12 Celestion green backs and 15 watt 12 alnico blues are so highly regarded for overdriven guitar applications. They warm up the overall tone a bit while retaining just the right amount of high-end sparkle. This is similar to what you were getting at with your Claypool sonic junk reference above.
Alembic-style electric guitars can get there through the right kind of rig, but the consensus among the guitarists I know is, they are better suited for cleaner, more articulate applications. If one is playing cleaner using this type of instrument, one could get away with a more hi-fi approach to guitar amplification, but IMO, they'd still have to be careful to tame the high end - which means no tweeters.
Acoustic guitars, on the other hand, are more like electric basses. They benefit from smaller, more efficient speakers and tweeters and cleaner amplification with a lot of headroom.