My Bigredbass is the deluxe (Three-stripe purpleheart / maple) laminate neck, mahogany wings with maple tops only, and FatBoys in the traditional Spoiler circuit, 34.
The Elan is maple neck with cherry pinstripes, and ash wings with maple top only, P/J Activators with the Sig circuit, also 34.
The Elan is way brighter as it's all 'white' woods, my idea to emulate a traditional Fender build, i.e., maple neck and ash or alder body. The ebony fingerboard always adds some zing! because it's so dense.
The Bigredbass is definitely warmer as the mahogany throttles that white-wood 'quack' back quite a bit. To me, it's the perfect all around blend: Not that dense presence of an all African-wood bass (like the Warwicks who often can sound like a tuba) and not as runaway bright hot as an all white wood bass.
There is a difference because the FatBoys sample a longer length of string (from the wider'magnetic aperture', see Mica, I get it!) than the PJ's, as well as their tone differences.
So I'd guess the mahogany is the leavening factor in what you're hearing, maybe some scale length in a small way.
You could get all scientific, put the same kind of new strings on both at the same time, play through the same amps settings for each, etc. After a while their identity will set in your head, and you'll either settle on on or the other, or use them where each is best.
J o e y