The Power On delay is the time the Harmony will wait before sending another command to that device. It will not prevent the Harmony from sending commands to other devices. However, the TV 4-5 seconds power on delay may cure your problem due to some annoying HDMI handshaking issues. Also, since HDMI is "two way", this connection can be used to communicate between devices to have one device turn another on, or tune to that input, etc. This can interfere with your intent (especially when using programmable remotes like the Harmony). Thus you should go to the user menus for both devices to turn this "auto-tune" feature off (sometimes called EZ-Sync, Viera Link, AnyNet, BD-Wise, or similar).

Note: You can change the powering order under the Activity > Settings > Review the order in which devices are powered on.

If these suggestions do not cure your problem, then as mentioned by rehaz1, you will have to contact Harmony support to have them insert a delay between the two devices powering up.