To adjust the bitrate of the resultant mp3s when converting FLAC with Audacity's Apply Chain feature, you do this:
MP3 export in Chains will export with whatever encoding settings were used last. So, for example, if you want to use MP3 export with a bit rate of 256 kbps, then before you start the natch process, manually export a file as 256 kbps MP3. MP3 export will remain at 256 kbps until you change it.