Riding with a saddle that is too high can cause the pelvis to rock side to side, causing some serious chafing of the crotch and inner thighs.
That said, if it is your preference and you've had good luck with it, then go for it. Everyone is different and has their own desired fit.
I know a number of people who actually prefer to ride frames so much too large for them, they have less than the required standover and must mount and dismount from the side, draping a thigh over the top tube when getting on and off the bicycle. Not to my taste but "normal" for someone who might have ridden "too big" bikes as a kid and grew up used to the feel. They generally mount the bike by placing a foot on the near-side pedal, push off and then swing a leg over as the bike as it accelerates forward. I know a number of my randonneuring friends in Japan prefer tall frames with horizontal top tubes and less than a fistful of seatpost visible.
I prefer to set my saddle position in relation to the bottom bracket first, then adjust my reach to the handlebars secondary to that with back angle in mind. I like to center my knee over the pedal spindle (KOPS -- Knee Over Pedal Spindle) and have a slight bend to my knee when the pedal is at the bottom of its downward stroke. One quick way to home in on the right bend for me is to place my heel on the pedal so my leg is fully extended. That way, when my foot is on the pedal (remembering KOPS), my knee is close to the right amount of bend. Everything that follows is down to simple fine tuning in a matter of millimeters. I'm real sensitive to saddle position and especially height and I find I must extend my seatpost a bit over time as my Brooks saddle's leather cover begins to shape and sag a little -- 3-5mm can make or break the fit for me.
Handlebar height and reach are determined after I get my saddle placement correct. I prefer the tops of my drop handlebars the same height as my saddle-top or no more than 50mm lower with stem reach being whatever gives me a 45° back angle with my hands atop the brake hoods.
Overall, my bike fitting methods are close to how I position my driver's seat in a car: Fore-aft so I can fully depress the clutch and accelerator pedals, then tilt the seatback until my arms are locked-out with my hands at the 12 o'clock position. That way, when I drive in my preferred 9-and-3 o'clock hand positions, my arms have enough bend to fully turn the wheel without locking out my elbows or over-stretching my arms.
As with all things, "your mileage may vary".
Best,
Dan.