Branched path tracing doesn't limit samples as such, it just allows you to set a lower base pixel samples number, then the various options, diffuse samples, glossy samples etc are multipliers of the base pixel samples applied to the relevant parts of the render. So you can easily end up with more samples. So if you look at the presets, you'll see high quality cpu (bpt) setting start with 8 pixel samples, while high quality gpu (non-bpt) uses 30 pixel samples.

The usual advice given to anybody who asks about improving render quality is bump up the pixel samples, and so the advantages of bpt, allowing a lower base pixel sample isn't used.

I think the trouble is for most of us we are really in the dark, since who wants to spend hours doing render passes to find the optimum setting in bpt, with all the possibilities as this is going to take longer than just setting a high pixel samples, start the render and go to bed! Especially as the best settings are likely to vary from one render to the next.

So have a look at your bpt setting, are the pixel samples much lower than those your are using with non-bpt, if not this is why the bpt renders are taking longer.