Heck, runabouts have a jeffries tubes running under the deck between the forward and aft compartments. I think it was Blaze of Glory we saw one them?
The Delta Flyer is a large shuttle, the runabout is a small ship. Most ships couldn't carry them at all, and I think it's almost a bit dubious even with the pregnant belly that the Armitage class can carry four of them.
Danube Runabout: 23.1 meters (DS9 Tech Manual)
Delta Flyer: 15.1 meters (seen frequently during 'VOY' from Season 5 and onwards)
For some of the other shuttlecraft (may or may not exist ingame):
Debuted during TNG:
Type 6: 6 meters (TNG Tech Manual, seen occasionally during 'TNG')
Type 7: 8.5 meters (TNG Tech Manual, seen occasionally during 'TNG')
Type 15: 3.6 meters (TNG Tech Manual, seen occasionally during 'TNG')
Debuted during DS9:
Type 10: 9.64 meters (DS9 Tech Manual, DS9 ep 'The Sound of Her Voice')
Type 18: 4.5 meters (DS9 Tech Manual, DS9 ep 'The Search Part 2')
Debuted during VOY:
Type 8: 6 meters (seen on occasion during 'VOY')
Type 9: 9.17 meters (seen on occasion during 'VOY')
Type 11: 14.64 meters (seen in 'Insurrection')
Type 1: 7.32 meters (seen during the run of 'TOS')
Type 3: 8.93 meters (seen in 'The Final Frontier')
All in all, it's safe to assume that the 'Danube Runabout' is the largest of Starfleet's shuttlecraft arsenal, followed by the Delta Flyer (which began as an unofficial Starfleet design, as a complement/replacement to the aging Type 6 and Type 9 shuttlecraft aboard the starship Voyager). I'd say in terms of which shuttlecraft is most modern, the Type 11 is likely to be relatively standard issue (unless replaced by 2409).
Still waiting on the SC-4 variant of the "Type 9" which was seen as Admiral Janeway's executive shuttle in VOY's 'Endgame'. That shuttle existed in 2404, so there's no reason to doubt that it may exist in STO's time period.
The Runabout's size is pretty well established... in the episode "Playing God," Jadzia states that the ship is 14 meters wide. With one dimension given, you just have to measure the studio model to find the length, 23M.