I think this used to work correctly. Nowadays, when I I split a transaction and one of the parts requires a transaction on the the other side, that is created as usual. However, I can't set the flag color on that linked transaction. The flag icon is not present in the list, and if I open it and try to set the flag it tells me I need to edit the other side. The other side does have the flag color I want, but it's not set on the linked transaction.
So, the flag color can't be set on this transaction, and setting it on the other side does not change it. Meaning there is no way to set the color.