I think Scotrail's policy should be that bikes may get on a quiet train if the nominal capacity is exceeded on the proviso the owner is warned they may be asked to get off and wait for the next train if it gets too busy.
Conductors trying to predict the future, i.e. how many bikes there may or may not be wanting to get on the train at any given platform up the line and at what point any other bikes already on the train may or may not get off is doomed to fail.
My usual bargaining chip is to promise to get off if it gets too busy and I'm causing an obstruction (I've never had to). I once nearly missed the only train on a Sunday from Thurso to Inverness (and therefore my connection home to Edinburgh) thanks to an obstreperous conductor who refused to allow more than 2 bikes on an otherwise empty 2 car 158 unit. Myself and another cyclist who hadn't got bookings would have been left stranded in Thurso (coincidentally it was someone I knew from Edinburgh Road Club). The conductor claimed it was not his fault but that "Inverness" (said in that reverential yet disdaining manner normally held for company management) were counting bikes off the trains and if there were more than the nominal capacity it was more than his job was worth. We negotiated on by promising to get off at the 2nd-to-last stop (Muir of Ord) and cycle the rest of the way to Inverness. We were wasily able to fit our 2 bikes alongside the 2 on the 2-bike rack that the train had with some imaginative bungee use. The conductor did come through the train at one point to check if we had remembered our side of the bargain.
Come Muir of Ord we played our ace and revealed that we had booked connections at Inverness in half an hour (including booked bike spaces) and there was no way to cycle it in time. With much huffing and puffing and not willing to hold the train up he grudgingly allowed us on to Inverness. Of course at Inverness there was not a soul on the platform (it was about 10AM on a Sunday) and the trains heading south were packed to the gunwhales with unbooked bikes.
I have heard that Inverness can get very shirty and threaten to call the police on cyclists on occasion if they dare to travel by bike.