Very nice guns!
In addition to the items you already listed on the Commander, it appears as though the following parts have also been replaced: grip safety (wide and appears to be a drop-in vs. fitted-to-the-frame part), mainspring housing (flat, is usually arched), and I agree that the safety lever is non-stock (it looks like it was a wide combat/target-style lever that was slightly thinned in width to fit the owner's preferences). In addition, it has a mag funnel added to the bottom of the frame; this may be permanently installed, or a temporary addition, held in place by the grips (I can't tell which by the photos you posted; look for a thin gap between the frame and the bottom of the grips if it is temporary). Edited to add third option: the magwell funnel may be attached to (or a part of) the replacement mainspring housing. It looks like the grips are also matched to the magwell funnel, or they would have more of a taper on the bottom edge, so the grips have been replaced as well.
Given the nature of the modifications, I'd also look inside to see if any work was done. In line with the other modifications already listed, I wouldn't be surprised to find that the feed ramp and barrel throat had been widened and smoothed, and perhaps the ejector replaced (both common mods for this type of pistol).
The value of the pistol will hinge greatly on the quality of the work that was done to it. If done well, you might be able to get $700-$900 for it in a private sale; if done poorly, then a knowledgeable buyer probably would only offer $200-$400 for it, as a rebuild project. Based on the offer you already had, and assuming that the person who examined it knew what they were doing (BIG assumption), it's probably worth at least $600-$700. Check inside the box (or in the log book) to see if there are any receipts from a big-name pistolsmith; if the work could be traced to a known 'smith with a good reputation, the value could be significantly higher.
A shop owner will always offer less than the true value, as he needs to leave room to make some money on the deal when he sells the pistol. If you want to get the maximum amount of money from the sale, you'll have to sell it yourself. If you want someone else to put up with the potential headaches (if you sell it, you'll have folks calling at all hours, low-ballers trying to get it cheaply so they can flip it, people from other states or felons who can't buy legally, etc.), then you'll have to take less money for it by selling/trading it to a dealer. You may get more money on a trade than cash sale; depends on the dealer, so ask.
Edited to add: If you have more than one magazine for the Commander, and you're going to keep the Officer's Model, I'd keep any extra Commander mags to use in the OM (just include one mag with the pistol sale). The longer Commander mags will hang out the bottom of the OM frame a bit, but it will give you a few more range mags for your "keeper" pistol; OR, you could sell them separately to make a few more bucks.