I do this quite a bit for species targeting. There's not a slam dunk strategy / single tool. I generally do self organized trips without guides. As such, figuring out sites, how to get to them, the lay of the land, what to expect where, and the best sites for the hard birds all kind of goes hand in hand. I generally will break it down to even province level within a country a lot of time when doing the needs lists, and then I'll use the hotspot explorer to get an idea of the names and locations of the hotspots, then I'll manually go through all the species and see what look like the hard birds and for the hard birds, what look like the good spots. It's a lot of work but you end up having an idea of what you're heading into.
The alternative is send a needs list to a guide and have them cook you up an itinerary, I guess.
Keep in mind that a bird that is on 1% of all Costa Rica checklists might still be an easy tick at the correct site - it's just that there might only be one or a small handful of infrequently visited sites for that bird. There are only a handful of possible ticks for me in CR and the most common is "only" on .6% of lists. Of those, however, two are easy if I were to go to the correct locations - Cabanis's Ground-Sparrow and Nicaraguan Grackle. Two more are very gettable if I were to go to Cocos Islands. After that come Tiny Hawk, Yellow-breasted Crake, Slaty-backed Forest-Falcon. A two week trip to CR targeting those three species could easily still come up blank. After that it's a handful of vagrants... so you really need to go through the list and understand which are the widespread birds, which are birds that you need to target, and where to best target them.
What you're asking for, I agree would be awesome. Something like a per-hotspot needs list. Then from that they could make a tool that would show you the hotspots within a region or country that have the most "needed" birds for you. I'd use the shit out of that