The short answer is that yes, you can setup the medium frame to be very similar to the small frame.
The reach and stack are the important figures that are hard to fudge.
In truth 700c wheeled bikes can only be made down to a 53/54cm size. Smaller than that they just fudge the geometry to make it look right on a spec sheet.
The difference that's confusing you is that the small frame has a steeper seat tube angle that's pushing the saddle forwards towards the handlebars giving a shorter top tube length on paper. If you go to the trouble of maintaining the same saddle setback then they are pretty much identical with the small having a lower stack/head tube length.
The medium frame will have higher handlebar height without adjustment and a good feature is that the medium frame will allow you to experiment with moving the saddle back giving you more saddle setback than present.
EDIT, OK, I was slightly confused and was only comparing the small to the medium of the same design but the principles still hold. The small and mediums are VERY close. In truth you can't build a good small with 700c wheels and they are just a medium that is fudged on way or another to make it look/seem smaller.
Last edited by AnthonyG; 04-24-19 at 07:08 PM.