One problem is that it’s not just Akkoma at that point, different software handles things differently and this can lead to unexpected situations for those as well, causing all kind of federation problems.
As for migrating in place, it has been done before from gnu social and from mastodon, but it’s not trivial as you already noticed, and you need more than just putting everything in a new DB structure. For example, you also need to keep things fetchable over their AP-id’s. And I suspect those to be very different on Misskey than on Akkoma. See also https://meta.akkoma.dev/t/migrating-an-instance-from-mastodon where this was also talked about.
In both cases, you can always try, but I do not advise it, it’s at your own risk, etc.