It is pretty common knowledge why they did this. Original plans for the BART had it traveling over the Golden Gate Bridge into Marin County. Due to high winds across the bridge, they wanted a wider gauge to prevent trains from tipping.
With strange, custom-construction-requiring stuff like this, I tend to wonder how much of it would be explained by "help self/a buddy get rich". It's practically guaranteeing that there's going to be a single company supporting it for all time, which is a potentially-extremely-lucrative business deal.
If that's the case, obfuscating the reasons for these decisions is a rational move.
It's a bit cynical to say this but running HSR on an incompatible network protects it against future politicians who may seek to sabotage it by merging networks.
This sounds similar to the reason why the Glasgow Subway runs on a 4' (1219mm) gauge: to stop it from being taken over by the numerous (at the time privately owned) railways around the city which were all standard gauge.