Rebecca - I am sorry to read of your loss.
It's very difficult to explain what's right or wrong in such cases as we deal with what's applied for rather than the thought process, options and decisions made re the property following a death. The following points may though help you
We register the legal ownership and it reads as if your parents were joint owners. When your Mother died the legal ownership passed to your Father.
The TIC you refer to and her/his wills relate to their beneficial ownerships. And when joint owners decide to be TIC they may apply for what's known as a form A/joint ownership restriction -
Joint property ownership: Overview - GOV.UK
I assume you have checked the register for the property and confirmed that they were joint owners and a form A restriction is present. If that's the case then there are two things to apply for if your Father is not the sole legal AND beneficial owner.
The first is to update the register with form DJP plus a copy of the death certificate. The second is to apply to cancel the form A restriction using forms RX3 and ST5. The two applications can be submitted together. There is no registration fee.
Our PG 6 explains how to do both -
Practice guide 6: devolution on the death of a registered proprietor - GOV.UK
Just follow the guidance carefully and don't over-think the form RX3/ST5 and follow the bulleted guidance
The application you have submitted will be waiting to be processed and that won't happen for some time as we have a backlog of certain types of work. But it reads as if the Transfer is not needed and as such, if you agree, you should contact us using our contact form and ask for it to be cancelled and any registration fee returned -
Public guidance: dealing with land and property - GOV.UK
Please do consider seeking legal/financial advice if you are uncertain as to what to do or what's best. We register the outcomes of such deliberations but cannot offer advice re the wills/trusts created and how such matters should be dealt with. Updating the register can be quite straight forward but deciding what's best and then how to do that can be complex.