Hi Nicholas
Like yourself I find that Sonic Pi 3, is much more easily taxed as regards Xruns than its predecessors, but I suppose that this is not unexpected as it doing a heck of a lot more behind the scenes that previously, supporting midi I/O and audio I/O
I have played around quirte extensively with differnt settings for the paramters in jackd, using qjackctl intially, and then committing the parameters to the command line within Sonic PI. Currently I am working at 96000 for the sample rate, and using 1024 byte buffer with either 2 or 3 periods. Even with these settings I get some xRuns if SP is taxed heavily.
This means that you have to go easy on using fx, especially if nested. Also some synths cuase more problems than others.
However I find that using midi to an external synt and then feeding the audio back into Sonic Pi works pretty well, and I have done quite a lot of stuff using this setup.
I have two pisounds, and I have worked quite a bit using modep on one of them, and Sonic Pi 3 on the other, and sedning midi across to synths in modep with the audio returned to Sonic Pi. You may have see `a recent project I did with this setup https://rbnrpi.wordpress.com/2017/08/25/a-touchosc-jukebox-for-sonicpi/ which created a jukebox for Sonic Pi, and this ensabled a wide variety of pieces to be played on Sonic Pi without significant xruns.
For anything really meaty I tend to use SP on my Mac which handles things with ease.
PS I find that using the clear command on Sonic Pi, can help to clear things a bit if you start to get a lot of distortion and breakups.