I use a lot of Acoustica plugins and yes, they tend to be very temperamental. In a mulit-region edit, I render the entire clip with the effect, and then cross-cut those sections into those specific passages where I want to use the effect. I might also consider running the plugin as a track effect if I had an edited assembly of clips to which I wanted to apply the effect.
Acoustica plugins are at least 64 bits of audio precision (I believe internally they may be as high as 80 bits). You could also render out your composite group out as a single Wav file at high precision and then apply Taupe to the comp’d file.
I do notice that bad latency reporting or the long look-ahead time of some Acoustica plugins plays havoc with the first 5-10 seconds of the rendered clips. I frequently have to clone a clip with an extra five seconds of silence at the front end in order to give Acoustica plugins a “running start” and avoid having an unwanted artifacts in the beginning of the rendered audio.