The normal way to install a VSR is to leave the alternator directly connected to the engine battery, always charging that one as is intended. Therefore there are no problems with alternator sensing, no matter whether it senses at the battery or at the alternator.
The VSR then, upon detecting a suitable charging voltage, will switch on, connecting the house bank to the alternator (and starter battery) and charging both. This can optionally be combined with a smart regulator (e.g. Maxcharge).
At least that's how it works on our boat and has been working well for many years now, apart from the VSR having died once in that time. I have replaced it with a Victron Cyrix-CT one and can recommend that.