In theory it is possible to get plans for a Skerry with centerboard - the Expedition Skerry CLC built for John Guider has a centerboard drawn on the plans. I've been trying to either get the Expedition Skerry plans or kit from CLC but so far haven't been able to. The expedition Skerry is wider than the regular model, has a deck and has a centerboard. You might look at the plans for the Whilly Tern (Wooden Boat Store) which I'm going to build since CLC is not responsive. The Whilly Tern is almost the same as Expedition Skerry though a foot longer.

Here is the Ian Oughtred Whilly Tern I am thinking of building in lieu of the Cruising/Expedition Skerry.

A centerboard would definitely be a good idea.  The daggerboard does not want to get out of the way of anything you might not see under the surface--I've been brought to an abrupt stop a couple times--can't be good for the board or the boat!

A centerboard will add more weight to your boat and change the interior configuration or space. If this is not a probelm it should not be a problem.

I would mock up the trunk and consider how the trunk will affect use and access within the cockpit.