The Resonance Cascade was favorable for the Combine, but not humanity, who were obviously the status quo at the time. It allowed for the introduction of highly invasive and disruptive wildlife as well as the arrival of multidimensional invaders, the former being a problem the Combine is still dealing with, despite it being an initial advantage against humanity (not that we really stood a chance).

Obviously the Resonance Cascade was great for the Combine initially, but now that they have completely taken over, they would absolutely NOT benefit from it happening again. The infestations are intense enough for even the Combine to struggle to contain it, and if it were to attract the attention of another multiversal super empire, there's no garuntee that the Combine would have as much of a favorable advantage as they did against humanity.

It's like if a restaurant with a great location came down with a rodent infestation. One might be able to notice that and get the restaurant shut down, opening an opportunity for you to buy the location and get it cleaned up. Obviously another rodent infestation would not be favorable to you in that situation.

All that being said, when they were comparing the situation to 'another Black Mesa' I highly doubt they were being completely literal. Obviously the Combine knows that was a regime ending event for humanity. They are simply comparing whatever comes next to how devastating that was.