The National Rail ticketing system is very old & very fragile, it broke for over 6 months in 2005, when an upgrade was attempted. The 3 month rolling window on sealed train times (T Minus 12) cannot simply be a data file transfer from Network Rail's master data system, the system is so old.
To deliver seat reservations, the TOC must subscribe all or parts of their train services to this facility, and the rules are 1 seat reservation for each ticket for that part of the journey. To provide cycle reservations a virtual coach was put on that train, where each bike space = a seat. Unfortunately this immediately breaks the rules (2 seat reservations for the ticket(s) on trains which have reservable seats)...
Staff need to be trained in the 'right' way to abuse the ticketing system to issue cycle reservations. For season ticket users with TPE in Manchester it can take 10 minutes to create a dummy ticket, on which the bike travels with its reserved seats, & voiding fares .... separately for each of the 10 trips..
The MixingDeck ticket sales suite used initially by GNER, had an operating feature which could manage bike reservations. Now the phone app systems are changing the options for this part of the ticket sales package. Likewise the increasing delivery of electronic seat reservation downloads to the train/guard's iPhone enables direct, real time reservations, rather than printing the reservations (often at a central location) and delivering those tags to the train, to slip into the seats, or for TPE bike spaces, under the coach identity label stuck on the window.... It really is that crude & improvised!
The final twist is that every day at 00.01
all of the seat reservations, & unsold AP fares are transferred to the host TOC, and with Cross Country the first to do so, the unsold cheap fares, were made available, online/via phone app Their social media them (& call centre) also secured a coup, by offering access through them to reserve bike spaces.
The fudged system also means that 2 clerks can double-book spaces through this offline process, as has happened on some Scotrail Oban trains.
GWR has put bike reservations in to their phone app upgrade, and were asking for cyclists to test this, for GWR services only.
Scotrail's proposal for the special bike carriages, also poses a challenge in managing the vastly increased by Never of spaces. Hence the reaction to the 'exclusive' story that broke in The Scotsman, before Scotrail & Transport Scotland had properly worked through and tested this aspect of the 'new' carriages.
@Rosie has the solution which the late Ian Pragnall used for booking groups on to West Highland trains in 1990's. He made all bookings with Fort William station - boosting their ticket sales, and getting access to staff with great knowledge of the available services, rather than a contractor with minimal training, and for the Independent resellers, tacit policy of avoiding transactions which don't deliver any income (e.g. Train line used to charge a collection fee where most TOC don't)