How to compare stability between 5‐methylcyclohexa‐1,3‐diene and 3‐methylenecyclohexene?
As far as I have read, in general, exocyclic double bonds (which are outside the ring) are stable for 3 or 4 numbered rings while endocyclic double bonds (which are inside the ring) are stable in 5 or 6 numbered rings.
As you note all the factors, more or less all factors are same in both cases, so it becomes a little handwavy thing.
Additional Reading:

Goumans, T.; Ehlers, A.; Lammertsma, K.; Würthwein, E. endo/exo Preferences for Double Bonds in Three-Membered Rings Including Phosphorus Compounds. Eur. J. Org. Chem. 2003, 2003 (15), 2941–2946. DOI: 10.1002/ejoc.200300120.

Fleck, B. Notes - Stability and Ease of Formation of Endo and Exo Double Bonds in 5- and 6- Ring Systems. J. Org. Chem. 1957, 22 (4), 439–439. DOI: 10.1021/jo01355a023.

Exocyclic vs. endocyclic double bonds in E1 elimination (although this one is not much relevant here).