I'm an inventory clerk and if I did your Check Out I would have assigned all of that as damage.
Holes that have been patch painted are visible, deliberate actions, unlike scuff marks that are part of normal living. You should expect to pay about a tenner per hole - not the whole house, the whole room or even the whole wall. It's called a proportional compensation charge.
A chip in a tile will have required an impact, dropped cup or similar, and is damage. Cracked tiles often are not as they could be down to the substrate. But tiles, on the whole, don't just chip. You pay for the repair.
Freezer drawers! I see a lot of these in rented houses. In my 56 years of life I have only seen one in my own home! DH pulled on a frosted up drawer, it broke, we bought a replacement. You should have spent the £20ish per drawer. The landlord is entitled to replacements, but you could argue that he can't have new for old. But as they are supposed to last for 10 - 20 years you would still owe him about 90% of their value.
Light fittings you should have had put back by a proper electrician. I would also hope you had one fit your preferred fittings as you would probably have negated everyone's insurance is not! You could be asked to pay for an electrician to put them back as was, or to be checked for fitness for use.
Curtains aren't something anyone would expect to be stained. They are a low risk item. So yes, you could be charged for cleaning or again a proportional compensation charge. Again curtains are expected to last forever so you'd pay a high % of the cost.
Landscaping! Your choice. The landlord could ask you to pay for it to be reinstated as was, remove the tree (as he now has to maintain it) etc.
Keys are a nightmare. Given you changed the locks instead of asking for a repair you have to replace ALL of the keys not just your tenant set. So if the agent held a management set and the landlord had one you need to replace those too. Often a landlord will just change the lock and keys again, and TDS etc will agree that is reasonable!
When you decorated with permission did they say that you had to put it back as it was when you left? That would be the normal arrangement. Stark white, magnolia and cream are always preferred in the rental market. If you did not the you could be charged for the redecoration. BUT you can easily argue that as landlords should expect to redecorate every 7 years you only owe about 50% of that charge.
Towel rail etc you should have reported and reported... if you did and have proof, like emails, then dispute that, as an ongoing issue from the beginning of your tenancy.
Basically, after 3 years in a brand new or totally refurbished house I wouldn't expect there to be much to report. Scuff on walls, maybe spillage on carpets and some settlement cracking. It shouldn't need redecorating or anything replacing as decor and furnishings all last longer than 3 years!
That and New for Old is not an acceptable charge and proportional charges should always be levied. Though again 3 years is not a great % of any white good expected lifespan.
I hope that helps.