It depends on what you think of as "fundamentally different". If you are talking protocol wise then yes, the idea is different. If you are talking about the technology used, then there are similarities.
The first one, where you encrypt a number is basically a challenge / response authentication protocol. As encryption is used the padding (e.g. OAEP) is specific for encryption and the actual message can be encrypted using the public key. That last part is modular exponentiation for RSA for both encryption as decryption.
The second one is indeed a signature generation protocol. If it is used for generating signature over documents it can provide non-repudiation. To do this first a hash over the document is generated. Then the signature specific padding (e.g. PSS) is applied, and then the private key is used for signing $^{*1}$. That last part is similar to decryption; it uses modular exponentiation as well.
So although both schemes use "RSA" one uses the encryption/decryption part (public/private) signature generation part and the other uses the signing/verifying part (private/public). Although the underlying technology of the decryption and signature generation is the same (the RSA trapdoor function that applies the problem of prime factorization) there are differences as well.
$^{*1}$ Ignoring container formats for this explanation.