Unfortunately, Basic Bot in Bizhawk is intended to brute-force basic scenarios for button meshing. The goal is specified by RAM addresses conditions, like the highest value. You cannot instruct it to change NDS settings.
Take a look at these submissions:
#6589: Arc's NES Who Framed Roger Rabbit in 03:48.11 - there is a big map where items spawn at pre-defiend spots, but at random. The input was manually brute-forced to get the best spots. The objective looks similar to yours if the map is not completely generated at random.
#8248: adelikat's NES Dragon Warrior IV in 1:56:29.29 - here, the whole game was examined for top to bottom, and a lot LUA scripts were written to automatize the process of passing each chapter in the fastest time. Basically, they was playing itself for a long time.
As you can see both of these are NES games, which means no RNG was manipulated outside the game. I don't think LUA scripts can change settings of a core, like the system timer, but if the same can be achieved by starting the game by delaying your input, then I don't see the problem in brute-forcing the game around that point. Nobody will reject your submission because of some delay in the main menu.
One way or another, you need to find RAM address which indicate the properties you need. Examine how the map is generated. Is the whole map is generated at once or only the location you being on? Is it restricted to 1 shop/hall or not? What about trees and other obstacles which may block your way? And a lot of other questions.
You will need to reverse-engineer the map generator and entity properties, like type of an object (grass, tree, river, creature, shop, town hall) and their coordinates. All this to know what exactly you need to get.
Also, respective LUA scripts have to be made in order to brute-force the conditions you need. Use Dragon Warrior submission for reference.
In short, a big amount of work has to be done, if you really want to achieve a perfect game RNG.
Otherwise, go with manual meshing and invest some time into it. Your submission will not be rejected because of an RNG that's far from perfect. Read this post to make this clear:
Post #532136
Good luck!
