Sorry about reviving an old thread guys.
Your point is made due to the use of lots of stock footage, something I was wishing the TNG Remastered would fix, and TOS Remastered did fix when it used a CG Enterprise to replace the pilot footage that crept in. I get the difference between Probert's ship and the 4-foot model, which was obviously thicker and had raised paneling to make it stand out on an SD medium. In such a case, they should use CGI to make one consistent appearance for the ship and replace any non-conforming shots fall in line at the minimum.
In relation to the alternate reality, several have pointed out that its scale appeared to change within the movie itself depending on the shot. Being fully cg, this movie could've rendered everything in a consistent size.