If you apply for a residence permit and are granted it, and you later apply for and are granted a residence permit on a different basis, the residence permit you already have is no longer valid from the time a new permit is granted. You will no longer have the rights the first permit gave you, when a new permit is granted.
If you apply for a first-time residence permit on several grounds at the same time, the permit that is granted first will be lost if one of the other applications is granted at a later time. If you wish to keep the first permit that has been granted, you must withdraw the other applications. You cannot claim back the application fee paid for the application(s) you withdraw.
Right of residence according to the EU/EEA regulations (see chapter 13 of the Immigration Act) is not a residence permit. If you have a right of residence according to the EU/EEA regulations, you can also have a residence permit, but not several residence permits at the same time.