The first thing that I look for as to why one bike measures faster ride times than another is if there is any aspect of the bike's comfort that inhibits the motivation to exert more toward achieving speed.

For example, a bike with fenders might have you maintaining speed where a bare bike forced you to slow down for a wet stretch of road.

Or one bike absorbs rough stretches of road better.

Or my biggest beef with most road bikes, that the saddle is too hard. Nothing slows my times more than a hard saddle.

If the Trek's combined flexibility and perhaps the tall bars have it feeling twitchy, that is one thing that will probably slow your effort over part of most road segments.

My long-wheelbase Nishiki and Steyr "sport-touring" bikes are examples of bikes that I can almost always exert to my limits without instability or discomfort, and so have also performed better on tough rides than reasonably expected for such heavy bikes. Not coincidentally, I found myself putting most of my mileage on these on our tougher back-road training rides. Both bikes also have what is likely the softest saddle available with tubular titanium rails.

Oddly enough, the Steyr with it's shallower angles was the twitchier bike, likely due to it's low-trail fork.
I first tried the longer stem, which fixed the stability issue, but left the steering to wander forcefully when riding uphill off of the saddle.
I then added a slightly wider bar, which seemed to fix that issue.
One thing that I'd already learned is that a wider bar tends to work better as the stem extension length is increased, in terms of the off-saddle steering dynamics.