I can understand the lever advantage, but what is wrong with having too much senisitvity in the brakes?

Brakes will be unpredictable and will tend to grab all of a sudden, rather than having controlled stopping.  You are not the first to try doing this.  I did it in 1975.  It was on a 70 Mustang.  I put the booster in and then lengthened the booster rod so it would reach the pedal. (It is too short for the manual pedal).  The brakes were overly sensitive, but I did not know there was any other way to do it.  Whoever owned that car when it needed a booster replacement probably cussed me pretty good because they too would have to weld an extension in the booster rod.

You are fortunate enough to know the correct way to do the job.

I can't say for sure on a '69 Mustang but, in '87, I changed my '68 Mustang from a C-4 automatic to a Top-Loader 4-spd.

I had to take the pedal support loose to get the clutch pedal into the hanger --there wasn't enough room to the left to slide the clutch pedal in with the pedal support bolted in. You may have to do the same to remove your manual brake pedal.

I also did this back in the '70s.  I added power discs to my '69.  I got everthing from a Fairlane, discs, spindles, prop valve and booster.  I started the job and had to have the local gas station finish.  they couldn't understand why someone would do this.  They heated up the manual pedal and bent it.  I think now that the booster was shot because the the pedal was very light and not firm.  I managed to not run into anything and do serious damage.  Now we have the Internet and Mustang Steve to protect us  from ourselves.  Happy Labor Day and don't get arrested.