They are incredibly similar in terms of overall quality, component level, and price.
I work on a couple dozen FX1 bikes each year(rim brake version) and based on that- I would lean towards the Giant for a few reasons.
The Giant has a better drivetrain in my view. a 2x crank is way more appealing than a 3x crank, given the quality of shifters and front derailleur. The 2x will make for less shifting issues and less adjusting needed.
The Giant has hydraulic brakes instead of mechanical. Both brake systems are entry level, so neither will be incredible, but given the work often required on entry level mechanical disc brakes, I would want to try the hydraulic option.
The Giant has a cassette and freehub, compared to the Trek's freewheel. This is a HUGE difference to me, as rear wheel maintenance is probably half of what I spend time on with the FX1 bikes. The FX1 wheels are very low quality as it is, so adding a freewheel only increases the potential for issues since it is inherently weaker than a freehub and cassette combo.
The gearing range for both should be fine for most all riding.
The Dfuse seatpost for the Giant is dumb- its just an unnecessary proprietary component, but that can be overlooked as its pretty minor and not an area where issues will typically be seen.