Mark -
If it were the only bike you owned and you were tight on money, then the XR400 would work OK as described. An XR650L would work better is your commute is more in town, and a KLR650 would be preferred if the commute had more highway or fast two lane in it.
Keep in mind my offroad-oriented DS bike is a street legal XR280; my road-oriented DS bike is a KLR650; my street bike with some groomed gravel road riding is a BMW R100GS. I've had a converted WR400, ridden the 650L back-to-back with the KLR and XR, and have ridden the XR400 and DRZ-E and DRZ-S
The DRZ-S is a good bike if money is not an issue and you can tolerate a small hard seat. The 650L gives you SIMILAR offroad capability to the DRZ in that it is the most dirt-oriented of the big bore DS bikes, but has a superior seat. The 650L is also available for much less used if money is a consideration.
When it comes to real road use of an XR, a friend of mine did a similar thing to what you describe to doing to a 400 - he sold his BMW just before a planned long vacation of riding. So, he took his XR 600 and did the following:
Big tank, low front fender, Avon Gripsters, geared it way up, Acerbis handguards with fairings, added one inch of foam to the seat, rubber footpegs, adapted dog packs as under seat saddle bags, and fashioned a tupperware lid as a fairing to the headlight assembly. He cranked out 3650 miles in 2 weeks on the bike on a ride from Colorado Springs up and around Montana and back.
How's that for versatility?