Allowing multiple daemon's per location sounds good to me, although I am less-enthused with comma-separated values. I'd much rather have configurable options support a one-to-many type that can be used for a select/multi-select field, for example, to choose one, or some, of the values. That would accomplish the same thing here, but it would be a completely different task.
IP management is a little more complex. I'm not sure how Multicraft chooses what port to use, but I imagine that it starts at one port (from a config setting in the Multicraft panel) and increments from there for additional servers, while checking to make sure the port is unused. This last part is what Blesta and the Multicraft API can't determine. Sure, we could have the module support a hard-coded or user-defined port range for a daemon, then randomly choose a port to use from the range, but that port could be in use by another multicraft server or a different service altogether. I don't see a way for us to determine whether a port we choose is actually available for use. Similarly for daemon IP addresses--it doesn't look like the Multicraft API allows us to determine what IP addresses are available to a daemon.
If you take a look at the Multicraft Settings, there is an option to choose how an IP is chosen when a server is created ("All Interfaces (0.0.0.0)", "Daemon IP", "Daemon FTP IP"; default "Daemon IP").
I think that Multicraft should allow the kind of IP/port management configuration you suggest, rather than Blesta. All Blesta really needs to tell Multicraft is to "create a server for me" (as it currently does), and the IP:port associated with that server should be determined by Multicraft and your configured settings.