Truro would be a very good place to pick up the car, as there is a rental office right on the station platform as you get off the train. The front door is off the street, the back door off the platform.
They are even open, or rather will open, when the Sleeper train arrives from London.
Looking at the list of sites to visit St Agnes feels a nice compromise as you basically have to cover from St Just to Bodmin and Padstow from this list. https://www.cornwalls.co.uk/poldark/filming-locations
Thus gaining a day by arriving on the sleeper would be a good idea.
Looking at your previous post is this still scheduled for late fall- mid October sort of time? You will be running into School Half Term if that late in the fall.
If looking for a cottage by the sea St Agnes itself (the main village) is up a hill from the sea. You want Trevaunance Cove. There is a separate little community down there, a lovely place to stay, I've stayed in the village but could easily imagine staying at the cove.
I remember some cottages down there so have just googled and come up with this local company- https://covecottages.co.uk/bookings/
I know it is not cottages but there is a really special pub down there with rooms- the Driftwood Spars- https://driftwoodspars.co.uk/
From the pub you are straight up onto the cliffs and the very obvious mining remains. You will love it down there.
It is only a 5 minute drive back up into the village for the shops, especially the Village Bakery.
How many of the 20 filming sites do you envision visiting?
Are you still coming up to the Lake District afterwards or concluding at Manchester, by the way?