Neck stiffness affects the string feel and tone. Floppy necks make the strings feel looser. Stiffer necks add clarity and focus to the B. You can make a neck stiffer with carbon fiber, stiffer woods, thicker dimensions etc.
Scale length to my ears affects harmonics. Shorter scales make it more difficult for the string to flex easily in the upper harmonics, damping them. This also results in the upper harmonics being further and further out of tune, with more energy dumped into the lower harmonics resulting in a warmer, thicker, denser tone. The attack is faster and with lighter strings the pitch rises more on the attack.
Longer scales allow more room for the upper harmonics to develop, they'll be more in tune, which is very noticeable when plugged into a tuner. The tone to my ears is more full-range, open and transparent. The attack is a little slower with less pitch rise. In general, you can play further up the neck without the notes warbling.
To be fair we've spent over a decade dialing in our strings for the 37" B, so they are pretty dialed in. However I have to assume that all the other string manufacturers have spent a good amount of time tweaking their strings for a 35" B so our comparisons are as accurate as I think you can get at this point.
To sum up: scale length is important, string design is important, neck construction is important, pickups are important, setup is important, body woods are important.
You can tweak one ingredient to compensate for the other and get good results, but in the end, why not tweak all of the ingredients to the max?