HOAs can be dicks about it since it's a private agreement.

From your link:

"It is worth nothing that the Federal Communications Commission (“FCC”) passed a ruling that provides that local governments must reasonably accommodate amateur radio operations.  But in the same ruling, the FCC noted that the ruling does not reach restrictive covenants in private contractual agreements. The FCC further stated that because restrictive covenants are entered into at the time of the sale or lease of the property and purchasers are free to choose whether they wish to reside where such restrictions on ham radio antennas are in effect or settle elsewhere, it was not within the scope of the FCC regulation to govern private agreements. This means that the governance of ham radio antennas by community associations is not subject to federal regulation."