I just noticed that when entering the nether (have not tried other dimensions yet), on my way exiting it all storms have completely despawned and the summon command disappears. I do not see storm clouds rebuild, yet if I load/reload or disconnect/reconnect to a server, the storms repop. Am I being impatient or does going into dimensions that the weather is disabled in break things until reload?

In my experience weather2 has had issues in the past for dimensional travel. I ended up fixing this with the config option ThreadParticleProcessDelay and set it to like 999999. I cant speak for versions beyond 1.7.10 for this though. In my 1.12.2 modpack this issue didnt show up AFAIK. It needs to be addressed in the code.