I don’t think there is a single source that will explain all of the above, nor do I think what I said is really just one topic, so you’ll likely have to research a few different related topics, depending on the level of knowledge you are starting with.
The first part of my statement above is really concerned with how sound waves resonate in tubes. Here you need to read a bit about the physics of flute acoustics. There are some good papers from the University of New South Wales on this, and various books on musical acoustics, such as Benade’s Fundamentals of Musical Acoustics, but they may not get to the level of detail needed to fully understand the above statement.
To understand why narrower bore flutes and whistles are physically longer than wider bore flutes and whistles of the same pitch, you will need to dig down to the level of understanding end correction. When you get there you will see that end correction is a function of bore diameter, and gets larger as the bore diameter gets larger. Most coverage of the topic stops there, but it is also important to understand that end correction is frequency dependent, and that for each harmonic component of a note there is a different end correction. A side effect of this is that as bore diameter grows the contribution of higher harmonics is reduced, resulting in wide bores having a loud fundamental, but weaker harmonics, and narrow bores having notes with richer harmonics.
There is a pretty good discussion of this advanced topic here, in the context of organ pipes, but if you need more introductory information first you should search for articles on resonance in open ended tubes, and end correction:
The last part of my statement is also about harmonics but about how they relate to musical temperaments in tuning. More specifically, it is about the difference between the size of intervals (particularly the major third, which determines the location of tone hole B2) in just intonation vs equal temperament tuning systems.
There are many sources that discuss various aspects of the above, at different levels of detail. If you want to do a deep dive that will cover everything, building from first principles, and giving you an interesting historical perspective, you might enjoy reading a copy of Hermann Helmholtz’s seminal work “On the Sensations of Tone”. In that case set aside a few weeks to absorb it, but then you’ll be well prepared to read all kinds of other material on the topic.
The last part of my statement is really just my own hypothesis that a maker who is more sensitive to harmonics will be more likely to make tuning and voicing design decisions that are influenced by the above harmonic considerations.