Do I have to submit the very same thing all over again and pay the £65 again to be able to get a resident permit card?
If by "resident permit card" you mean a permanent residence document, then yes. You must have a permanent residence document before you can apply for naturalization. If your only document is a registration certificate, you are not yet eligible to apply for naturalization.
(Note that the permanent residence document is not a "residence permit" because the document itself does not confer permission to reside in the UK; it only serves as evidence of permanent residence status, which arises automatically.)
As noted at the first link, you can normally only apply for a permanent residence document after you've lived in the UK for five years, and you can only apply for naturalization after you've had permanent residence for at least one year (therefore, after you've lived in the UK for six years).
There are some exceptions, however, in which you can get permanent residence before you've lived in the UK for five years. If you qualify for one of these exceptions, I believe you can also apply early for naturalization, one year after having qualified for permanent residence, but the site doesn't say this explicitly.
There is also an exception allowing earlier naturalization if your spouse or civil partner is a citizen of the UK.
Home Office already has got all my details, why would I have to submit everything again?
This is necessary because the home office needs to evaluate whether you meet the criteria for permanent residence. For example, someone could arrive as a worker and received a registration certificate on that basis, but then leave their job and live in the UK as a student or self-sufficient person. In that case, to meet the criteria for permanent residence, the person would have had to have comprehensive sickness insurance. You therefore need to prove in your application for permanent residence that you have been a "qualified person" for a period of five years; your registration certificate by itself does not demonstrate this.