Different equations produce different results as expected, but each equation is used with different guidelines for preheat, interpass temperature, etc.
The carbon equivalency equations are simple one tool in the welding engineer's tool box. Like any toolbox, there is one tool the serves a purpose better than another. The equation I used was just one of several and it was handy. It was meant to be an example of a carbon equivalency equation that listed all the alloying elements present in the alloy system you are dealing with. The guidelines used with the equation are going to "kick in" at different Ce than a different equation with different guidelines. I use the one I listed becuase the guidelines take into account the hydrogen level of the welding process and filler metal as well as the degree of restraint.
The equation you listed simply has different guidelines that are applied at different levels of Ce.
As for grain size, that has more influence on toughness than weldability. The welding procedure used can influence the grain size, hardness, and toughness of the completed weld. The grain size is not going to affect tensile strength or guided bend test results significantly when dealing with the two materials you listed. Both have significant levels of carbon that are on par with each other. The influences of chrome and molydenum on the Ce are to a lesser extent. Simply put, you can add carbon or other alloying constituents to the base metal. The one that has the most significant affect on weldability is carbon, so it may be better to reduce carbon and add other alloying constituents in its stead to maintain good welding characteristics. However, chrome and molylbdenum are much more expensive than carbon.
I wasn't able to plug in the numbers because I didn't have the actual chemistry of the 4140 available. I am surprised that the two alloys were exactly the same. I wouldn't expect that. Again, it is a case of picking the right tool, oops, equation for the alloys you are working with. That can be a problem when they are from two different alloy families. What you found is one area that you must consider. If you were to apply the same equation to austenitic stainless steel and carbon steel the results would be totally misleading.
Best regards - Al