The timings on the nexus bus stops are based on the quickest scheduled journey. The rather odd timing of the 45 is based on the very first trip (0529 ish?) which doesn't encounter much traffic (cars or passengers). This explains the wide discrepancy to the 46 and 47.
In general terms, if a service has an evening variation, that's the point-to-point timings nexus use. Personally, I think these timings raise customer expectations too much. I'd much prefer they used general daytime timings, as they are generally more robust for connections/ journey planning, etc. and if a bus arrives at destination point earlier than customers expectation, this would certainly excite less comment...
RE: Bus stop numbers