I have an SC58 with 53/10s, and the Sig with 408s. Just going in humbucker mode, I hear very significant differences between them. Partly of course, the SC58 has a thicker body, but they're both stoptails, and I play them through the same amp.
I hope I can describe what I'm hearing accurately, but later this week if I have some time I'll record something so the comparison can simply be heard.
In any event, here's what I hear, assessing bucker mode only...
Bridge:
In 'bucker mode, the 408 bridge has significantly more treble and a hotter output than the 53/10 bridge. The treble does tend to mask midrange and lower midrange, but I find that the 53/10's frequency balance is much more midrange-oriented, even with everything on the guitar full up. Also, the 408's attack on the onset of the pick is sharper, where the 53/10's attack is more rounded. Again, this can be attributed in part to the HF response, but I think there are other factors at work as well.
Neck:
The 53/10 and 408 are a little closer here, but the 408 still has more output and sounds a lot brighter. The 53/10 has a more jazzy-bluesy sound full up, where the 408 is more of a rock tone, though with the tone control and volume pulled back, it can do the jazzy-bluesy thing nicely. But it's not the same. The 53/10 has a beautiful clarity and shimmer, the 408 has a nice pick attack and also cleans up nicely, but it reminds me more of a single coil (even in humbucker mode), sort of a P-90-ish type of overtone but without the noise. To my ears, the 53/10 sound is huge and full on the neck, but that might be the guitar it's screwed onto.
Obviously, it's fairly subjective, and different guitars are going to sound different. So there's that.
This is just my take on things, and everyone's mileage will probably vary.
But if someone asked, "Which of your guitars have the least overlap?" I'd have to say the SC58 with the 53/10s and the 408, with the Artist V coming a little closer to the Sig Ltd than it does to the SC.