I would suggest, if this one time event is such an annoyance, that the extension's startup script be adjusted to check if X is already running. If so, do not overwrite the current X server, Instead, exit.
This would have no impact on normal operations, .i.e, from booting or loading X while not currently running X.
Additionally a link to the startup script could be placed in the user's path together with a note in the .info file for such manual X server initialization. Such would not be much different than other distributions requiring some X server setup before initial run. Such would only be required when an alternate X server is loaded from within an already initialized and running X server.
When the base fully supports normal operations, then the base should be preserved and not cluttered with extension references or requiring needless extra code.