I just discussed this with a Rav:
There are 2 reasons why fish and meat are Sakona. First, as brought by the gemorah is a practical reason, that one could choke if a fish bone gets stuck in meat – it could happen by a fish bone alone, but there is more of a chashash by meat. The second reason is in the Zohar that it is a ruchnius’dike sakona – I don’t know the details.
The difference is that the first reason the sakona is only mamash by eating them together, although lechatchila we should be choshesh for everything, however bedieved will be more meikel (for example cooking in the oven together). The chumras according to this stem from Chamura Sakanta Me’Issura. The second reason prohibits anything even bedieved.
This also would have a nafka mina by ein mevatlin apparently.