Yes, Couperin's music is wonderful, isn't it?
How to register his pieces on the organ can be problematic if you don't have exactly the kind of instrument Couperin played, and almost none of us do.
First of all, in an ideal world where I did have a nice French classical organ, I'd try to follow the indications as closely as possible, HOWEVER, those indications are not as exact as they would seem. If, for instance, the score says, "Recit de Cromhorne," there are still a lot of variables that are not indicated, and I believe intentionally so. Couperin probably knew OTHER French organists would play his music, and their instruments would be slightly different than his, so he would indicate that it's a Cromhorne piece, but leave the details up to the organist and the instrument at hand.
What are some of these variables? Well, for one, do you use a flute with the Cromhorne or not? I don't have documents in front of me, so I can't make direct quotes right at the moment, but there were French organists who wrote about how to register these pieces, and sometimes you'd use the flute, sometimes not. It helps the speech if you have problems with it, but depending on the kind of flute, it might make the Cromhorne sound too fat and tubby. It depends on the instrument. Then there's the problem of what to accompany it with. . .how about flutes 8 and 4? or maybe just an 8' flute depending on what you need to balance it? Or add a 4' Principal? There are lots of possibilities, and all within the realm of what Couperin probably would have recognized.
Then you have the Plein Jeu and Grands Jeux. These are supposed to be registered in a very specific way. Without getting too detailed, the Plein Jeu is the Principal chorus, and the Grands Jeux is the cornets and reeds. But even among French Classical instruments there are differences, so they might have to be tweaked a bit.
Then we come to the problem of what if you don't have a French Classical organ? For instance, the Hook and Hastings I play is very different, and is missing very many of the stops you really need. What to do? Well, what I do is not play too much Couperin, but I still do once in awhile. There's not a cornet to be found on the instrument, but since the Open Diapason has rich harmonic development, I sometimes play an "Open Diapason en Taille." But I don't make the claim that it is anything like what Couperin intended, and I probably would not do it in a recital.
So the short answer to your question, for me, is that if I had the right stops, I would not change things, but would tweak as necessary to make it sound right, just as the original French organists would have done. I would not turn a "Recit de Cromhorne" into a "Recit de French Horn" just because I wanted to try other colors. The pieces were intended for certain colors. However, if an otherwise unsuitable instrument can be coaxed into playing these pieces, and it was for church, I'd play one once in awhile, not very often. If the instrument just can't come close, perhaps like a symphonic organ, I would just forget about playing Couperin there.
Does that hit on what you meant to ask?
Tom
