"...there was any security reason for this..."
No security reason at all. I wouldn't worry about allowing the PTR record to be created for the records internally.
If you were hosting your own Reverse DNS record zone for your public DNS, I could understand this being a potential issue. However, any public nameservers you host should not be Windows-based, should not be domain members and should be located in the DMZ, so you've got a bigger security problem with or without the PTR record issue if you are doing this!
"...if A records were only registered manually too, would this break anything..."
It won't break anything - you just give yourself a lot of administrative overhead. Over time, if the records are not maintained properly, the IPs on workstations and other devices (particularly if they are assigned by DHCP) will become outdated and your DNS will become a mess.
-Matt
