Thanks @wthelen for this report.
Hm, I am wondering if this problem is the same as the one reported in Why the subplot second panel is getting cut? - #5 by geodacharya.
If I run your code with a PyGMT dev version + GMT 6.5.0 and ghostscript 10.03.0. The map isn’t cut off. However, in both topics, higher gs versions are used. So, maybe there is a problem with higher gs versions. I have to make an environment with gs higher than 10.03.0 and test on my own.