If, in your case, you want to treat all even numbered vertices different from all odd numbered vertices, then you could use gl_VertexID built in GLSL variable.
You could pass in two modelviewprojection matrices, one for type A and one for type B, and apply the one based on the least significant bit of gl_VertexID.
if ( gl_VertexID & 1 ) ...
If there is no fixed pattern for which vertex number gets which treatment, then you just need to add an additional vertex attribute like DMGregory proposed.
If you don't want to do that, and if you are passing 4-float coordinates with x,y,z,w you could even encode the special treatment in 'w', and reset it to '1' after detecting the special case. (Or even hack in a large offset in x to signal this. But that's the ugliest option.)