Typically (meaning, these observations are not universal but are most-always true):
When it comes to dealing with the City, any HOA requirements don't matter - the City has no jurisdiction and indeed, no duty, to enforce any HOA and/or subdivision covenants and/or agreements. Those are entirely between owners and the HOA's.
If this is a PUD - a Planned Unit Development - then it's an animal of its own. When a PUD is created, the owner of the development and the City enter into an agreement that creates specific rules/arrangements for that particular development, and generally negates the rest of the City new-construction zoning ordinances. The owner typically agrees to build to such and such code, follow such and such setbacks, make lots such and such size, install such and such utilities, etc., and in return the City usually agrees to pick up the installation of the rest of the utilities, or pours the sidewalks for them, or builds the streets, or builds a park, etc. So it's not at all anything like a typical subdivision. Only the rules specific to this particular PUD that the City approved/adopted are the ones that you (and your neighbor) will follow. The entire rest of the zoning code (probably) does not apply, only the rules written and recorded when the PUD was adopted.
Just as an example to show you how jacked up PUD agreements can be - we have a newish PUD here (that was signed before I started here, thankfully) which is built on the 1999 BOCA building code at a time when my City was enforcing the 2009 IBC.
All that to say - don't go quoting the City code to any City officials or any City boards before knowing that what you're quoting applies. If your house is in a traditional PUD, whatever is in the general zoning regs. probably doesn't matter.
And I still don't know why you care how big the neighbors deck is. There's no way that deck makes your half of the townhouse worth any less money.