No, you should never install vCenter using the IP address. There is something going on in your case and I think it has to do with your installation process.
By the way, thanks a lot for helping!
You know what is strange... After i install vcsa, i go to 5480 management page and check NTP - its perfect. Then, i reboot and get that error. I just tried to acccess 5480 port page and noticed that NTP is completely wrong there! I changed setting in appliance management and rebooted vcenter again - no success.
You know what is strange... I have another installation of vcenter 6.5 (same version) in another firm. Network topology there is completely same, and vcsa reboots w/o issues with NTP pointing to Mikrotik router. The strangest part is when i log there on Appliance Management page, Last Health check reports correct time, but when i press on a "Time" page, its shows wrong default Timezone (-3 hours from what i am in). But still Everything works there.
The only thing I can think is that device isn't providing NTP services correctly. I've never seen that behavior anywhere as you have noted. Can you try another NTP source, even if it's external to your network? Use the IP if you can, not the FQDN.
Jesus christ! I did it. Thank you man! Its really stupid to be honest, but using external ip address of NTP server worked.
To be honest i dont get it why vcenter is so demanding...
This is proof that the internal NTP server you thought was functioning correctly actually is not. vCenter, like so many other enterprise applications, depends on correct time keeping within the datacenter to function properly. This isn't a case of vCenter being any more demanding than other appliances--time keeping is extremely important, and when you don't keep good time or your time source is tainted, bad things begin to happen.