You got it backwards: the vaccines specifically targeted only the spike protein, while natural infection created different antibodies against all parts of the virus.
Novavax COVID-19 vaccine never targeted specifically the spike protein, and instead focused on boosting the creation of various different antibodies. It is also the least effective.
The current breed of mRNA vaccines targets the spike protein, and the TRIM21 gene. Some of them also attack the S protein directly.
All of them work to boost various antibodies. The "targets" are in addition. By targeting the spike protein, the attack hits the RNA of the virus, not just the protein. The entire cellular structure of the virus breaks down. The same with TRIM21 targets.
The bodies natural defences never targeted the spike protein, and instead focuses on the N-layer, not "all parts of the virus". These natural defences rarely manage to cause the viral cell to decay, they tend to work by slowing reproduction instead.
Novavax's vaccine was also spike-protein-only, the difference between theirs and the mRNA ones was they created it artificially in moths then extracted it for the vaccine instead of generating inside the human body.
Novavax was called "protein subunit", not "vector" - you're probably thinking of J&J and AstraZeneca which were adenovirus-vector - but also still just encoded the spike protein.
