You use a Collection to apply a Maintenance Window to machines. Once that Window is applied to a machine, then it's applied to that machine, any Deployments on any Collection that machine is also a member of can take advantage of any Maintenance Window that the machine has picked up.
During that maintenance window the machine will look for any active, applicable Deployments that fit within the Maintenance Window (by comparing the Max run time set on the patch or install to the remaining time left in the Maintenance Window) and then run them one by one (re-evaluating the remaining time at the end of each install).
It doesn't matter which Collection applied the Maintenance Window, or which Collection applied the Deployment, just so long as the machine is a member of both Collections.
So it depends what you mean by "references a collection". When you double click the collection in the console and see the list of machines that match its rules does the machine in question show up in that list? If so it will pick up any MWs or Deployments set on that collection, if not then it won't. Inheritance isn't the important thing, whether a machine is a member of a collection is.