Whilst the beginning and the end sections seem straight forward I realised when plotting the gpx tracks the figure of eight route from Kings could if you blindly followed the track lead you into the wrong direction if one long track. I know nothing of the geography of Wales so none of the places make sense to me. Hence my splitting of tracks in 8. Also looking at Google street view to be vaguely familiar with where the controls are.
As you say, a single big track can lead to tired mistakes choosing the wrong branch if the route overlaps at all. On BCMs of old (and possibly still now, not sure) it never mattered which route you took going North from Kings YH, indeed some people used to out-and-back along just one of the routes. (I've no idea if this is still possible as there may have been new controls/infos added or things moved around.)
I personally dislike splitting a ride in to one track per control as it just increases the chance of messing something up (not uploading one section, etc) and the faff at each and every control. If I forget to use the downtime at the control to sort out the GPS for the next section then I'm left faffing with the GPS as others are ready to leave.
For the BCM I think I split it into two with the break at Menai. I just had to remember which way to go after leaving Kings YH as there's a bit of shared road for the inbound and outbound. (But then I was using a yellow eTrex H when I did the BCM with a point at every routesheet instruction.)
Perhaps an over reaction to lack of familiarity but the I know that feeling when you cannot find the control.
This is the main reason why I always plot my own routes from the routesheet, using OS maps (streetmap.co.uk) and Google Streetview. It's still not perfect (plenty of stuff has changed since the last Streetview pictures were taken, and things can look a lot different in the dark) but relying on a downloaded GPS track alone is going to increase your chances of struggling to find unfamiliar things in the dark.