Equipment Profile Adjustment

I brewed a stout recipe yesterday using 3.94kg of grain in the mash tun adding 11 litres of mash water and 17.5 litres of sparge (fly) water and ended up with approx 25 litres in the boil kettle.
I also steeped 340g of rye grains in 2 litres of water which I added to the kettle after 50 min of the boil. I didn't sparge this so I had about 1.5 litres of additional fluid added to the kettle.
I was aiming for 20 litres in the fermenter but only ended up with 17 litres.

I have assumed 4.5 litres of boil off in my equipment profile and lose about 1 litre in the bottom of the kettle that I am unable to drain because of the concave bottom and hop debris.

Should I adjust my boil off losses, and where in the equipment profile is the kettle/trub loss etc accounted for?

I would recommend making the adjustment to the boil off rate in your equipment profile.  Then follow it over the next couple of brews to make sure it is correct or to 'tune' it to what you normally encounter.  I have a spreadsheet where I track the critical parameters and use the average to tune in or confirm my equipment and mash profiles.

The lost wort that you cannot drain out of your mash tun should be input in the section titled "dead space volume".