Hi. When you toilet train your rabbit you want to have all hard floor in his enclosure and only soft in toilet box (or boxes). Rabbits like to pee on soft so no blankets/rugs around during the training. In your situation I see you have tales there so just leave them uncovered so as was suggested above you can keep it clean and put any poos and paper towels soaked in urine into his toilet and clean urine spots with 5% white vinegar (cleans, disinfects and removes odour) so only toilet box will smell like toilet and the rest of his floor won't, rabbits like peeing where they can smell their urine.
Also as already said I would move his toilet box where he likes to pee, they usually like corners and choose one corner, but you can add another litter box and place two on both sides.
I personally never use puppy training pads also most of rabbits can chew on them and get a blockage from ingesting plastic so it's a no for me.
I would get a piece of lino (preferably textured so he can have better grip for his fluffy feet). Lino must be bigger than his area so he can't have access to edges because some rabbits (actually too many of them) like chewing edges and can get very sick from chewing lino, same with plastic.
The size of his area is fine but his plastic gate is a joke most rabbits (except of the very lazy ones) would jump over it easily, and he is only 3 months old so not even his full size yet. I would recommend to invest into a metal playpen much higher, I use baby fireguard panels 66 cm high even some rabbits can manage to climb over them, they are very smart!
Same like in this link I can't post photos this is 66 cm high and made of panels you can connect then into a long fence very useful. You can get secondhand much cheaper as well
https://www.smythstoys.com/uk/en-gb/baby/safety/safety-gates/babylo-classic-fireguard/p/129094
For toilet training is good to limit his territory, I don't know how far you want to go with changes and how much are you willing to invest, but thinking a bit into future, he will grow and he can be neutered at around 6 months (some vets would do at 4,5 months if he has his testicles fully dropped and weights enough) so you have about 3 months ahead you want to stay clean I believe. Standard rabbit cages are tiny and not high enough some people use dog crates medium to xl size and attach an x-pen to them, you can safely lock your rabbit for night or when you are not home so he can't jump over the gate and get into a trouble. Or cc grids are quite popular here you can build quite a large housing with them. There's a thread somewhere in Housing section you can find plenty of ideas there.