Finally fixed in Supernotes 3.1.2 
Just to note though, the second example in the OP (LaTeX parsing) is actually “correct”, in that what you have created is not actually inline LaTeX with no content, but rather the beginning of a LaTeX block with no content (and no closing tag). Our parser actually happily processes the rest of your card as LaTeX even without a closing $$, so we’ve left this behavior as is.
Highlights (==) and spoilers (!!) should be good to go now and properly align with their rendered counterparts.