Depth is a non-issue in most of the Maine anchorages and coves you'd visit. I would not waste your time taking the boat to Bar Harbor. NE Harbor is much more transient friendly and the free Island Explorer bus will take you anywhere on MDI.
Some insider tips:
Robinhood Cove - Ignore the marina end of the cove and head down SW into the long cove, good holding and peace & quiet. Beware worst mosquitoes on the cost reside on the Georgetown and Phippsburg peninsulas.
Love Cove Ebenecook - on the West side of Townsend Gut. You'll need to anchor.
Seal Cove - up the Damariscotta River come in at the top half of the tide and you can get over the shallow spot.
Seal Bay - Vinalhaven - One of the most beautiful spots on the coast.
Long Cove Vinal Haven - Beautiful spot if you go up in.
The Basin Vinalhaven - DO NOT take your boat in there. I've been in multiple times, mostly by dinghy, but now that I am older won't do that again in the big boat. I suggest anchoring in Long Cove, next door, and taking the dink over for a lobster bake on one of the many small islands that dot the Basin. One of the most beautiful spots on the coast.
YouTube - The Basin - Vinalhaven Island, ME
Winter Harbor Vinalhaven - Simply amazing you can go way in past the big rock and no one else will follow you
Carvers Cove (Not Carvers Harbor) best sunrises on the coast

Sand Beach - Marshall Island (great day stop)
Frenchboro / Long Island - Lunt's dock has the best lobster on the planet. This is is second best hike on the coast. I have ALWAYS had excellent holding just outside the moorings beyond the ferry dock.
Wreck Island - Merchant Row
McGlathery Island (West Side) - Great beach for a lobster bake
Hells Half Acre (North Side) - Great spot -

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Isle Au Haut Thorofare - Moorings put money in coke bottle, best hiking ANYWHERE on the coast. A few of the moorings are tight but I have seen 60+ footers in there. Plan to spend a full day hiking the trails of Acadia. Duck Harbor is nice but has lots of granite and can be poor holding have seen more than one boat on the rocks there.

Duck Harbor view from Duck Harbor Mtn.
Burnt Coat Harbor Swans Island - Go in and pass the rental moorings near the big building. GO past all the fishing boats and anchor up in the cove roughly across from the church. No morning lobster boat traffic and a nice peaceful spot.
Over Rated Spots IMHO (as a local):
Camden
Pulpit Harbor
Perry Creek
SW Harbor
Rockport
Tennants Harbor
Rockland
Bar Harbor (stay at NE Harbor and take the free Island Explorer bus system to anywhere on MDI including Bar Harbor.)
Under Rated Spots IMHO:
Round Pond - Muscongus Bay
Castine
Belfast
Northeast Harbor
JO Browns North Haven - Fox Isle Thorofare
Stonington - Anchor off town and can provision at the store which is right off the town docks where you can tie your dinghy