There is no direct tool to confirm if your node is functioning properly. You can use tezos-node config show to verify the running config before starting. Watch (ie: read) the output when the node starts as it will tell you if RPC is listening and on what port.
Use this site: https://www.yougetsignal.com/tools/open-ports/
to determine if the P2P port, 9732 is ...
Flextesa's mini-net has an option --add-external-peer-port to allow other nodes.
It has been used to test 1 node joining the sandbox (incl. as a baker → in order to test Kiln).
I don't know of any attempt to make larger networks but it's worth a try.
The docker implementation with tezos is bad. https://gitlab.com/tezos/tezos/-/issues/548 It does not allow for many configuration parameters to be customized, and hard-codes many parameters too.
For your specific case, this can be solved by using an external mountpoint as the storage for the node like this: