This concern arose while testing the new WildFly 8.1 runtime added to stacks.yaml (JDF-727). This itself is ok, but Rob pointed out another concern:

If a new runtime requires a new runtime type in the future and we add this to stacks.yaml, older versions of JBDS/JBT will not recognize this runtime type, but will still gladly offer it to you for download through Preferences -> Runtime Detection -> Download. When you choose the path of Server -> New, the runtimes offered for download are restricted to the given server type, so we're safe there.

So this is what we should do:
The list of runtimes offered for download should always be restricted to only those runtimes that are defined in the given JBDS/JBT.
E.g. if EAP 7 needs an eap7 runtime type in stacks.yaml, but this type is not available in JBDS 8, JBDS 8 should not offer EAP 7 for download.