My case is a bit extraordinary in that my subs are integral to the speaker design and the speaker itself. The midrange driver handles above 100hz, and the integral subs are 10hz-100hz. So indeed the 65hz frequency of a cellos low notes is changed by turning my subs on and off. Previous to this I've integrated subs into my system crossed over much lower (in the 45hz range). There also, it seemed to make a difference to me in how the cello and instruments occured that reached similar lows that are NOT necessarily included in the spectrum covered by the sub. Sorry that I can't explain it beyond that, but that's what I recall hearing. I certainly admit that I could be influenced by expectations. The mind is a powerful thing.I don't know that your situation is "extraordinary" as there are a number of speaker systems that are designed from the ground up with a sub. However, I think the general gist of the discussion has been toward the question of adding subs to stand-alone speakers.
As for a lower crossover point, keep in mind that there is rarely a brick wall at a particular frequency. If your sub accurately crosses over at 45 Hz, it is almost certainly putting out a noticeable amount of sound one octave (90 Hz) and even two octaves (180 Hz) above the crossover point. The amount depends on the respective slopes of high and low pass filters involved for the speaker and sub respectively. (And, even if a sub crossover has extremely steep slopes, that in itself introduces another set of problems to deal with.)
I sold stereos back in the days when most amps had tone controls and it was extraordinarily rare to find a customer who did not like the change in sound that came from nudging the bass and treble controls up to 1 or 2 o'clock.
Whether or not this is the effect you're experiencing is hard to tell unless you can compare your system side-by-side with a live cello (to continue the example in use) or perhaps use some RTA analysis of your room response with each configuration.
Ultimately, your only question is "are you satisfied?"