It depends on your bio mechanics. I don't mind running a little short but I am a mountain biker. It "can" put pressure on your internal quad. This strain can cause the MCL to ache. Its worth trying.It feels like that when I first get on the bike, but it doesn't last.
I'll raise the handlebars when I've knocked out some other costs. Maybe I should forfeit a little power in the meantime and lower the seat a couple of inches. Would that do any harm to my knees?
The gist, since you can't go shorter at back is to go taller and closer in front
Even just something like this could make a world a difference
And if it still hurts you can go to a bar like this
Which gives you a lot more hand positions to play with.