As to the mods possibly degrading things...hard to say. On some decks folks offer both "transparent" and "warm" mods, so at least one mod must definitely alter the sound in a way that is less true to the recorded signal than the stock unit. But the result appears to be a sound most folks prefer.
How about this...buy stock from Oade. He still gets your business, and is saved the trouble of modding. Plus, if you decide to have him mod it down the line, it may well cost more (also you'll need to ship it again, and wait again) but if you have him mod it right as the warranty runs out, you don't lose any coverage and maybe even gain an additional 90 days. Although I agree, most often if the unit is going to fail, it will do so in short order.
And yes, it's unfortunate there are apparently no comparisons out there of stock vs modded R44, or few good comparisons for any of the mods for that matter.