Is it permissible to establish the رجعة (return to marital union after a revocable divorce) and have witnesses present in order to obtain a new marriage certificate after one year has passed since the رجعة, even though the court stipulated the wife's presence?

If this was the first or second divorce and you took your wife back while she was still in her iddah (waiting period), then the رجعة (revocation of divorce) is valid, and she is your wife according to Islamic law. Documenting this iddah is another matter that does not affect its validity, and it can be done at any time; it is also possible to have witnesses attest to it.