While it's certainly true that the scenarios were designed for the unmodded game, not only was base FfH2 updated several times after the scenarios were first introduced, but it remains an unfinished product. Kael was planning further bugfixes and AI improvements, as I recall, before stopping further work. It's been a long time since I played regular FfH2, but I do remember the AI changing radically after one of the patches, and not in a good way. During a war with the AI, it would retreat and evacuate cities, leaving them undefended or nearly so. Then it was building monster stacks of doom. Full disclosure, I've never tried the scenarios myself, but given all the changes post-introduction of the scenarios and the unfinished nature of the base mod, it might not offer the best playing experience for the scenarios any more.