> both the skyscraper land owner and the parking lot land owner are being charged based on the investments made on the skyscraper lot.

The difference is that while they pay the same, only the skyscraper owner is making any serious revenue. The skyscraper goes from being a tax liability to a profitable asset, and the unproductive parking lot goes from a profitable speculation vehicle to a tax liability.

The owner of the disused parking lot is then incentivized to either develop it, or immediately sell the property to someone who will develop it.