I cannot help but wonder if lack of sustain contributes to a darker tone? Consider the strings contact the nut to the bridge, I wouldn't think it makes a difference either with the tuners unless the original tuners absorb some of the vibration? There is also the idea behind the tailpiece and the weight and type of metal used impacts the tone.
Since I seldom play clean enough to notice such nuances, it doesn't really impact me. If I'm playing clean, I'll have some sort of modulation going, delay, reverb, chorus all of which impacts the tone. Of course, when playing dirty, I really don't notice because I'm hearing more of the amp and pickups more than anything else.
Curious though, why did you change the tuners out? I have the Heritage branded tuners on my H150 standard but only considered swapping the tuners for locking tuners for quick string changes. However, I think I need to learn the luthier method of stringing up a guitar instead of the loop, pull, and bend over the string method.