I'm not sure why you provided IOS commands , but the only downside of enabling bpdu guard on AP ports is that someone could send a bpdu and the port would go into 'err disable' state which would 'DOS' that AP.
It also prevents someone from unplugging the AP and plug a switch since Meraki do not support 802.1X auth on trunks so you don't have any other way to protect your network from that behavior.
Some enterprise prefer 'security' over user experience. I have mixed feelings over bpdu guard on AP but it can be done.
Also if you use SecurePort ( RIP SecureConnect ) it will not override STP settings , so It would keep the bpdu guard from an access port.
EDIT :
TLDR : There is no good or bad answer to configure bpdu guard on Meraki AP ports. That's my opinion. Some may agree / disagree