Fixed in commits 8f65957, 89f0ead and 072cb36 respectively (backported to V12.8 in 41edaf2, f1dea52 and 697a2ea).
In the case of #1, I didn't implement an absolute "it always pauses", but rather, it pauses if the user has the "pause after backwards frameskip" option enabled. (This option is enabled by default.) Additionally, if you don't have this option on, while it won't specifically pause, it will no longer unpause either. Behaviour when loading a replay is unchanged.