Grazhdanskiy Shrift is an attempt to revive the font, which altered the structure of the Russian alphabet by the reform of Peter the Great. The project is still in a draft. Any contributions are well-come and highly appreciated at
Github or here. In practice, the font will contain 2 fonts (using the style set) to reflect the major changes that occur in the font after 1710 year.

Comments
First results (Github)
Perhaps finding more print samples at higher magnifications of the original would also help in making that decision.
Yes, you are correct that most typefaces are designed according to choosing one of those two alternatives, not mixing them from letter to letter. And, thus, most likely, the original implementation of Peter the Great's revised alphabet also shared this characteristic. But to delay the decision in the design process as part of an effort to avoid making the wrong decision is something that I cannot be inclined to criticize too harshly.
Hmm... Well one solution, I suppose, would be to make separate fonts for the optical sizes, but then I guess it'd be too cumbersome to use multiple fonts. You could, however, put different optical sizes for the characters in the font as alternates.
It's your decision, though. I'm simply trying to offer some suggestions.
That is what the size feature* is meant for.
*) Whatever implementation, OT feature, OS2 table or whatever is in fashion right now.
Off topic: what tool did you use to produce these figures?
All this is a matter of choosing technology and personal preferences. Perhaps the process can be improved and certainly someone else would choose a different approach - an approach with other tools.
Anyway, I just wanted to share a link to a free font that's not dissimilar to this. It's called "1725 Unicode", and it's downloadable here: https://www.fonts-online.ru/font/1725-Unicode
It's sort of interesting to see how your font and "1725 Unicode" differ, the main difference being is that your font is a cleaned-up version of Peter's civil typeface, while the other font is directly digitised from the original examples.
Perhaps when your font has been released, we'll be able to compare the two more thoroughly.
I made a sample adjust splitting the arms and then making them overlap to compensate the illusion. Just a rough draft, in fact.
By the way, I was not able to find the font in your site, as it is informed in Github fonts folder. I had to download the project in Github and open the ufo font in FontLab VI.
* I learnt this with Frode Bo Helland in an old Typophile discussion about the Nordic ø. A single tip that made me understood a whole universe. Thanks again and again, Frode.