I can understand criticism of docker specifically from a "requires root and daemon" perspective (rootless daemonless container runtimes exists) but this is such an odd take, using outdated software is completely unrelated to whether or not you use containers. Why would long lived VMs be better if they're also using old versions of software?
I agree mongo is overhyped and attracts a lot of web newbies who only know javascript and don't want to think through schemas, although one interesting newer feature of mongo is time series collections -- unfortunately they are a bit buggy but they're getting better seem like a legitimate non-relational use case.
"widely different" seems like a stretch e.g. ECS is pretty directly translatable to docker compose, and if you do cross-platform builds with buildx then I don't see why doing the building locally or on a cloud service matters much.
If you like git annex check out [datalad](http://handbook.datalad.org/en/latest/), it provides some useful wrappers around git annex oriented towards scientific computing.