Choosing path #2 isn't a panacea either.
WebCore, like any suitably large subsystem, has bugs that sometimes have to be worked around. If it's compiled in to the app, Omni can compile in workarounds for any bugs in the version they're using. If they use the system version, they need to build in workarounds for every version a customer may have (meaning every version Apple has shipped for supported versions of MacOS.) And you'll still have to update this as new versions of WebCore are released to customers.
Second, it dilutes the value of the product in the eyes of some customers. If your app is a wrapper around a system-provided component, can you justify the cost of the product solely on the quality of that wrapper?