Not necessarily. The ability to request or modify a seat assignment, however, would be restricted once the gate takes control. Now GAs can block seats, which might very well render as a general "unavailable" or "taken" on EF or AA.com, but they would appear differently on the seatmap in the host.

That said, I have noticed occasional inconsistencies between the seatmap when viewed in AA's partition versus the Sabre/GDS partition (which sites like EF and Travelocity use) when close in (i.e. 1hr - 30 mins) to departure. Anything inside of 15 minutes is much more likely to have inconsistencies as GAs are trying to fit people into seats, especially on an oversold flight.

But generally, you should always see an accurate picture of the seat map.