When you use Bootstrap with lineNumbersInTable=false you get line numbers and the line height is consistent. The only downside is when people use Firefox with copy and paste (see Mozilla issue I referenced above).
That would be nice. And it should work with Bulma too. And with every other CSS library.
You can either find the conflict in the library and override it, or export and modify the Chroma CSS with:
hugo gen chromastyles --style foo
and set this in your site configuration:
[markup.highlight]
noClasses = false