Hi All,
I have a Seery delrin, that, with my embouchure FWIW, is almost spot on on C and C#, but a little sharp on the F#.
I have another Lejeune flute, that's much flat on the C# but very well on all the others, with the same embouchure.
This got me curious as to what are the factors the makers consider before choosing what notes to favor (or sacrifice). Is it the relative proportion of the notes in the repertoire, or an artifact of the flute they may have borrowed design from, for example.

TIA for opinions.

I think it was Terry McGee who once explained the differences between "traditionalists" and "modernist" makers and the tuning of each of their instruments.
I think a modern flute should be spot on and there really is no need for these "quirks". So my guess is it might have to do with flutes that were copied or with the mentioned difference above. A flat C# could probably be brought in tune by re-setting the cork a little closer to the embouchure hole (a millimeter should be enough) but that will influence how strong the flute sounds and it might influence other notes but when making a flute for myself I tune it in such a way that the C# in the 2nd octave is very slightly flat so I get the strongest possible low D and just need to "push" the C# in the 2nd octave a little more. But that is a note rarely needed for ITM. I do like a flute however that is tuned for two and a half octaves and not just 2 octaves.
I think it is more or less normal for the C# to need a little more push -- it can be avoided by making the top hole a little bigger but that will in turn make the C natural too sharp with a standard fingering. That's why they say -- flute (and whistle) making is always a compromise. For example -- if I want an in tune C nat with oxxooo -- the top most hole of the flute should be rather small but that also means that the note can get "veiled" and weakened or it tends to be flat. My preferred flute which I made for myself (cylindrical however so not all the rules for conical flutes apply) has a huge top hole and huge holes overall which makes for a booming, almost boehm-like rather clear and "hard" sound but I need oxxxxo for an in tune C natural in the 1st octave -- the bigger the holes, the bigger and clearer the sound but cross-fingerings will work less well (which was the main reason for the switch from a cylindrical bore to a conical bore when flutes developed from the renaissance to the romantic era -- the holes became smaller and that, together with the conical bore made cross-fingerings possible to get all the notes needed for the music of that era). When it is just a transitional note, oxxooo will do but it is very sharp. However the nice thing about that hole size is that you can play C nat in the 2nd octave (not the first!) with just one finger oxoooo and also the 2rd octave is in tune with the standard fingerings up to three notes. Those are just my limited experiences with making a couple of flutes for myself in the basement with very primitive means and tools.
I am sure one of the reputed makers on this board can give you much better explanations. And the physics involved will be a little different for a conical flute. But the basic rules still apply I guess.