I've had my Checkpoint ALR5 for 6 months now and I've used it a lot.
I'm going to use it for a 1400km trip to the French Alps in February and I've kitted it out with Bontrager Racks front and rear and Ortlieb panniers so I can camp on the way.
I ride it with the chain stay adjusters all the way back to lengthen the wheel base and provide stability. I've also got full Bontrager mud guards and yes, there is a toe overlap.
I've swapped out the rear derailleur for a Ultegra RX GS version (medium cage) which allow me to run an 11-42T cassette. I have also put Absolute Black sub-compact 30-46T oval rings up front. Be gearing with 35mm tyres has increased from 27.24 to 19.40 inches. It's significant. Last week I did a 550ft climb that peaked at 19% with no problems. I'm not particularly fit and my bike/rider/luggage was on the limit of the 125kg Trek recommendation.
I use it for everything. With the panniers I do all the little journeys to the shops that I used to do in the car. I'm looking forwards to riding it next summer with some knobblies on round my local trails.
For test purposes, I did a cross country ride with the local bike shop on my MTB (and got a KOM!) and then rode the same route the next day on my Checkpoint. With all the stops negated and even without the group faff, the Checkpoint was quicker. It was an eye opener!
My only other upgrade will be a dynamo hub for my trip - Hunt Superdura with a SonDelux hub. Other than that - it's a great bike and I'm even thinking about selling my road bike as I simply haven't used it since the Checkpoint arrived.