Not exactly sure sure what you mean by alters the tone? As compared to what? An Albert Lee sounds like an Albert Lee. You can alter the tone in the PUP choice by selecting either the Duncan single coils or the EB MM90's. Is there something you want to directly compare it to?
Now there may be some slight variation between the tone with the circuit engaged or if you take the battery out and leave it unpowered and out of the signal path (Maybe NorM or someone can chime in here with some additional circuitry insight) but then you get back to single coil hum issue. I have never tried to A/B my AL with/without the battery, but who knows could be interesting?
With respect to the neck, I don't thik it feels anything like the Sub, not only in profile, but the fact that the Sub neck is finished vs. raw with oil/wax. Each of the EBMM necks have a distinct profile with the AL apparently coming closest to the AXIS. There are some recent threads regarding neck profiles you may want to search with additonal neck comparisons and opinions.