When filing a VFR Flight Plan, where/how do you include intent to use a Class B transition?
Since VFR flight plans are only used for SAR, and your route would only matter if you aren’t talking to ATC, I would file the route you intend to take if ATC denies you the B transition—or refuses to talk to you entirely.
If they do talk to you and grant the transition, then there will be a clear record of your actual path, and nobody will bother to look at (that part of) the route in your VFR flight plan. Or any other portion of your route where you have Flight Following, for that matter.
Note that, for calculating ETE and required fuel, Murphy’s Law says you should use whichever route is longest.
If you’ll be getting a WX briefing, mention the possible diversion to ensure your briefer checks that area too, but realistically, you won’t get in if there’s anything there serious enough to matter.