Well, standover should never be how you "measure" a bike. If you can get a foot down with one foot on a pedal you're ok in that respect.

Going to 650c wheels will lower the top tube, it will also reduce cornering clearance. If you're riding fixed, that's a VERY big concern. (pedal strike on a fixed gear more often than not involves you meeting pavement)

I just looked up the geometry on the kilo TT. Wow, it's long. 503mm top tube. Heck my 50cm SST-AL is 515. Then again, that's not what you're complaining about. Sounds like you've got some remarkably short legs there buddy :-)

If the rest of the bike fits, I'd say suck it up. Track bikes by nature are taller than your typical road bike, as they require higher BB heights, so you're getting what you asked for. :-)