Could be, but honestly it seems like the real estate people see North Station, Downtown, and the Seaport as entirely separate markets... it does mean that Fallon might do the last Fan Pier office tower on spec if he has the means.
The general trend is that big established firms (PWC, Goodwin Procter, BCG, Cengage, etc.) are consolidating into shiny new single-tenant (or nearly single-tenant) Seaport buildings, while smaller firms (e.g., The Globe, Bullhorn) are taking space in the multi-tenant buildings Downtown. A great example of this dynamic is that when the relatively small Boston Globe returned downtown they took a chunk of the space that relatively large Goodwin vacated when they moved to the Seaport. If you follow that chain, whichever firms eventually move into the Globe's old space in Dorchester will be able to in a sense point to Goodwin's new building in the Seaport as the factor that made their leases possible. When relatively large GE went shopping in Fort Point they took the space that relatively small Bullhorn vacated when they moved Downtown. Rapid7 is an example of a rapidly expanding smaller company leaving Downtown for a big lease in a shiny new (nearly single-tenant for now) North Station building. Their old space Downtown will probably be filled by an assortment of smaller, slower growing companies
There is plenty of movement across Downtown / the Seaport / North Station, so you can't say they're different markets. But there definitely is a sorting taking place along the spectrum of firm size.
Amazon is solidly on the "big established firm" end of the spectrum, so it makes sense that they're looking in the Seaport. Remember that they recently took 150k sf at 253 Summer in Fort Point, so another Seaport office would make sense for them. (This why I have South Station tower + later South Station phases + South Station Expansion office + MassDOT parcels 25-28, along with Seaport and Fort Point properties, as my pick for the best Boston HQ2 location).
The issue here is that developers want to land the big anchor tenant. They'd rather have one company taking 500k sf than 30 companies taking a combined 600k sf. And since the bigger established companies looking for big leases are focusing on the Seaport (and to a lesser extent North Station) submarkets, it's a little harder for developers to get traction for Downtown parcels.
I'd say a bigger issue, however, is that the Seaport parcels have
much shorter construction timelines than, for example, One Congress. In the Seaport, you can sign a big lease based off of a render and move in in maybe two years. One Congress, meanwhile, won't be ready for occupancy for at least twice that long, probably longer. That's a big deterrent... If Amazon wants space in the short- to medium-term, they're much more likely to get it built and ready on time in the Seaport than at One Congress. The Hub on Causeway office phase will have the shortest construction timeline of the bunch, so I expect that to get filled before One Congress even breaks ground.