The company that laid my flooring advised that there were one or two areas that needed levelling compound applied. They recommended (and supplied for me to apply) a latex-based system. It mixes up a little differently to water-based compound, spreads much better, and cured significantly faster. The cured compund is supposed to have a little "give" to inhibit cracking, especially in the places where the skin is very thin.
I don't remember what the brand name was, unfortunately. Maybe a local flooring company could help you to source some?