When using either Freedom of Scotland or Highland Rover on Caledonian MacBrayne you simply show your Rail ticket at the time of boarding (that said its worth checking CalMacs timetable as a small number of routes require booking
https://www.calmac.co.uk/calmac-summer-timetables).
In terms of the validity for Freedom of Scotland and Highland Rovers (and its worth noting I've not found this in writing) I've been told that the inclusive validity is only for the specified days as per the rail validity, but that the discounts available with these tickets are available for the whole period. Whether that's correct I'm not sure!
When I arrived at Mallaig I was told by the Calmac staff they I had to obtain one of their tickets before boarding. The ticket office issued a nil cost Calmac highland rover 10 day return Mallaig-Armadale ticket - you have to hand in the relevant portion when boarding the ferry as they use it to know how many passengers are on board.
I didn't need the return portion as I was going back via Kyle.
I did the journey sourth to north with a detour to Portree a couple of weeks ago.
Day 1 after using the Euston to Glasgow sleeper (FTW one was fully booked) I travelled on the 08:21 to Fort William.
Fortunately I was not going on to SKye that day as high winds meant the ferry departures at Mallaig were delayed/cancelled.
Day 2 I caught the 08:30 train from Fort william to Mallaig then caught the 10:45 ferry to Armadale (incidentally for car passengers this & the next 2 sailings were fully booked)
The 11:40 bus was arriving at Armadale as I came off the ferry - plenty of time to catch that.
If anyone is going to Kyle this bus gets to Broadford at 12:08 and the 12:10 connecting bus from there to Kyle is waiting across the road - it normally won't leave until the bus from Armadale arrives (the driver said it only goes if the one from Armadale is more than 15 mins late as that bus connects into the train at Kyle).
I stayed on the bus until Portree where I had lunch - I then caught the 15:23 Citylink coach to Kyle where I had 55 minutes for tea (there is a good tea room round the corner from the bus stop) and a look round before the 17:13 train to Inverness. The next day was to Thurso & back.