I’ve found manual payment methods, are not currently supported with the multiple entity feature.
In the docs, its listed as "third-party payment methods are displayed only on checkouts and for markets associated with the primary entity, with the exception of PayPal."
which makes sense since this is a Shopify Payments powered feature.
However, manual payment methods is a 1p feature, without any external connections or dependencies.
This seems like an oversigt, or possible something that wouldn’t be too complicated for Shopify to support (Multiple entity + manual payment methods).
Especially since multiple currency + manual payment method has been supported since last year. Either that, or at least update the docs this limitation.
Use case for the above, is as simple as enabling merchants to offer a wiretransfer option as payment option. This will currently only work the default business entity.