I used the world datapack defined in this Reddit post as a starting point: https://www.reddit.com/r/minecraft_configs/comments/hoakfc/after_a_lot_of_trial_and_error_i_finally_managed/

In that download, the separation and spacing for "custom:tower" appear to be at the default settings (1 and 0 if I remember correctly). I noticed that the structure is logged in the biome json (worldgen>biome>custom>hills.json) as a startable structure, but not in the dimension json (dimension>custom>custom_biomes.json) in the structures list. Since I wasn't certain what the doubled "structures" object was about, I tried both of the following when adding "custom:tower" to the dimension json:

"structures": { "structures": { "minecraft:ruined_portal": { "spacing": 4, "separation": 2, "salt": 34222645 } }, "structures": { "custom:tower": { "spacing": 4, "separation": 2, "salt": 34222644 } } }

and

"structures": { "structures": { "minecraft:ruined_portal": { "spacing": 4, "separation": 2, "salt": 34222645 } }, "custom:tower": { "spacing": 4, "separation": 2, "salt": 34222644 } }

(both behaved exactly the same as far as I could tell)

When loading the datapack up at world creation, the world generated without errors but the custom dimensions were not recognized by /execute. However, when generating a single-biome world using the relevant custom biomes, the world generated as expected, with the structure separation and spacings defined in the dimension json working as intended.

I have a vague suspicion that this may be related to MC-187904 which prevents custom dimensions from replacing existing dimensions and also gives no errors on world creation.