Will the company put you in a flight to HND and make you travel from there to NRT (train, bus, taxi?) if the ticket prices are cheaper or will them try to keep you flying to NRT as much as possible?
No, in my experience they don't really penny-pinch like that. If the timings work out for you via CDG or DUS then you'd just ask them to route you via either of those and you'd catch your ANA flight to/from NRT. If the timings don't work out and you'd prefer to go via LHR or FRA then you'd just ask them for that and they will pay for the bus to and from HND.
All of this assumes you are using the C Class option. Clearly, if you're using a ZED ticket then you sort it all out yourself and you're responsible for the fares to/from HND.