Can you preserve/can tomatoes of various sizes together?
Your intuition is correct here: cannng recipes are developed for a given chunk size (within a small range). If your recipe was developed for large chunks, the small ones will overcook and not taste as well, and if it was for small ones, the large won't heat up enough in the middle and thus it is unsafe.
Your options here are to:

sort the tomatoes into cans and use different processing times (unless you happen to find two recipes with the same time for large and small tomatoes because of different jar sizes)
cut up the whole tomatoes until they are roughly the same size as the small ones
find a recipe for hacked tomatoes and cut up all tomatoes before preserving them.
use a recipe for large chunks and see if the small ones still taste good enough for your personal standards

Hot water canning tends to be more forgiving than pressure canning, so if you find a recipe specifically intended for hot water canning tomatoes (hint, it will also require acidifying them), it might have a wide size range - you may test it and see if you are OK with the quality of the small chunks.