Closing Letter question

It probably depends a lot on what your contract with them says.

If there was a "punch list" period during which you were to report issues and they were to fix them, and that time period has passed, then it's probably time to sign and let the warranty department handle it.

If there was no such period, then I'd contact them and very nicely indicate that there are a few new issues that you've discovered that you'd like to have squared away before signing off on an otherwise fantastic house. (i.e. be really nice about it, and they're likely to keep you high on the priority list, be angry about it and they'll drag their feet.)

You don't sign off until you are happy. You already live in the house. Builder needs you to sign something. Being reasonable, you have no incentive to ever sign anything now that you live in house unless you are 100% happy. Note too that when you sign off builder may be done unless there is a glaringly big issue - which the 2 you noted aren't. Also note that warranty company may not cover pre-existing known issues. (pretty sure there is no chance they will)

Your (2) recently discovered issues aren't unreasonable concerns. If you approach the contractor and request they be rectified before you sign-off there shouldn't be any difficulties.

This will only happen if there was a contract written and agreed upon that stated this would be part of the building process. Most contracts won't detail every phase of the job. It should mention that the work will be completed to "code standards" (or words to that effect).

Your contract is what will allow you the legal right to with hold any payment if work is sub-par, but it also ensures that a customer can't continue to squabble over minuscule irritations.

Regarding the toilet; in my area the toilet needs at least 15 inches of space on either side of the seat center.