Note that my bike (the red Thruxton in OP's post) doesn't use the BC battery tray (the tray I use is from Deus Ex Machina in Australia), so how BC are going to do it might be different. But this album
shows how I've got the electrics/wiring hidden away. Basically everything except the regulator/rectifier sit in the tray (in a bit of a spaghetti mess) along with the battery. The reg/rect. is bolted underneath the tray. Again, BC may do this differently.
Personally, I've never had an issue with the wiring and wet weather getting into the tray area, and all my external wiring (e.g. to the regulator/rectifier under the tray) uses wet-weather connectors (from Eastern Beaver).
I've stripped a few things out of the wiring loom (AI system, wiring to the original R/R for example), but I think I've got enough room between the tray and seat that I could fit a stock, complete wiring loom with all the associated bits.