A deed would not be used to perfect a security interest. It must be filed legally but it is usually not used to perfect a bank's security interest, that would be the mortgage so it would not have to be included in the filing fees on the TIL.
If I recall in some states a warranty deed is the same as a mortgage or deed of trust. Also, if the title is being transferred as part of your loan transaction you most definitely have to file the new deed with your mortgage to perfect your lien otherwise the lien (mortgage) would not be in the name of the property owner.
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The opinions expressed are mine and they are not to be taken as legal advice.