Reproducible: always
Is a regression: no

Steps to reproduce (Sample attached):
1. Create alert and wait until it shown.
2. Get alert size using alert.getHeight() and alert.getDialogPane().getHeight()
Expected behaviour: alert.getHeight() returns window size with decorations, alert.getDialogPane().getHeight() return window size without header and borders.
Actual behaviour: both heights are the equal, but when trying to close dialog methods return expected size.