Regarding your second suggestion, I'd prefer to keep them roughly the size they currently are because it'd be more consistent with general symbol sizes but also, as you mentioned, it would be closer to the original.
Keep in mind that in actual typefaces diacritics are never that big. You're willingly choosing to err on the side of Cherry's laziness / lack of expertise from 30 years ago. This is just one example; arguably, even worse offenders are Cherry's original Russian Cyrillic legends, the Greek word-final sigma legend, etc. It's a good thing that those legends aren't used in modern keysets anymore. They would look out of place on sets with modern quality expectations and level of attention to detail, and it would appear as if someone just hadn't put enough time and effort into doing the research on what those legends should look like. I know how much attention to detail you put into your sets, Gok, which is why I think that you should fix those legends.
If you'd like to keep the glyphs consistent with sizes of other symbols, then make the base characters larger and diacritics smaller. But imo, just reducing the diacritics' size would look great. Just make sure it's an actually typographically correct glyph in the end. As anyone who types Czech on a daily basis will be able to tell you, those characters should not look like they currently do in the renders.