@RunnerVince
You say : "Nor do I remember whether they were Gatsby or Sierra or another of the 50 name variations out there."
You also say : "I think I'm just an OCD perfectionist . . "
Also, you do NOT say what TYPE of Sierra/Gatsby/other kit you are concerned about.
The differences between a Sierra TWIST and a Sierra CLICK are very significant.
My experiences with other pen makers here on IAP is that the majority of them tend to be OCD types . . . and that's not a bad thing.
The very fact that some people are attracted to pen-making is a real reflection of their OCD tendencies.
There are so many "little things" that go into making a pen attractive . . and even making a functional pen from a kit . . that one could make a case for saying that ONLY OCD-TYPES SHOULD TAKE UP PEN-MAKING.
It would take at least a pamphlet-length document to even begin to address the issues that you raise in your opening post above.
Firstly, you absolutely MUST take notice of whether you are handling the components for a Sierra, a Gatsby, or other of the similar kits.
Each kit (Sierra, Gatsby, etc.) has some differences/quirks in appearance/behaviour/operation that quickly become noticeable.
Yes, there are similarities, but . . . IMHO . . . it is not possible to deal with problems without knowing specifically what kit you are referring to.
As an example, you do not say whether you are dealing with the TWIST or CLICK versions of the Sierra . . . as one of your BRANDS of kits.
There is a very significant difference in the problems you can encounter between the two versions . . . TWIST or CLICK.
Also, you use terms like "small fraction of a millimeter" and "a thin 1/4" protruding from the nib" . . . there is a huge difference IMHO.
You need to talk in terms that more closely tell us the level of precision that you are striving for.
You do need a pair of machinist's vernier calipers to be successful in the making of pens and diagnosing some problems that occur.
If we stick to thousandths of an inch as our units of measurement, then 1/4" amounts to 250 thousandths of an inch, whereas one millimeter amounts to about 40 thousandths. So what is meant by a small fraction of a millimeter ?
In making a physically attractive looking pen, it is often necessary to be concerned about matching dimensions of components to within about 2 thousandths of an inch in some . . . but not all . . . considerations.
The making and assembly of a kit pen is very often about matching the dimensions of the kit components that you make or modify to just that sort of tolerance in order to achieve the best possible appearance and functionality in all respects.
Of course, you CAN achieve an "acceptable" result without full attention to this kind of precision and accuracy.
I know that it might be hard for you to specify your goals but you must try to do so to a degree that more nearly represents your problems.
For us to interpret your post and write pamphlet-length responses is not going to be well-received in this thread.
Let me try to address one issue. The brass tube that Berea supplies with their SIERRA TWIST pen kit has a length that is very accurately controlled, probably to an accuracy of better that 0.001" from one kit package to another IDENTICAL kit package. I believe that the same is true for the SIERRA CLICK pen kit. But, between the two types of kits, TWIST and CLICK, if you machine your pen blanks to a difference in length of 0.010" you will notice that difference with the CLICK kits but you will be unlikely to notice the difference for the TWIST kits.
That fact is just a factor related to the internal mechanisms and their differences between the TWIST and CLICK.
One additional issue . . . the differences in the protrusion of your refill for differences in brass tube lengths (caused by you not by BEREA) . . .
If you are making CLICK pens, you can easily cause differences in brass tube lengths from one pen to another of 0.010" or considerably more.
And even a difference from pen to pen of only 0.010" can be noticeable.
You can easily cause such differences if you are not EXTREMELY careful in your trimming the blanks. You know how you glue the blank onto the brass tube. Usually, you start with a blank that is a LITTLE bit longer than the brass tube and then you TRIM the blank down . . . IDEALLY to the EXACT length of the brass tube that the blank surrounds. Well HOW EXACT is "EXACT" ? We are told to trim carefully until the exposed end of the brass tube JUST BEGINS TO SHOW A HIGHLY GLOSSY BRASS TONE. Can you see the easy possibility of OVER-TRIMMING thereby causing the blank to be a TINY BIT TOO SHORT with the result that the REFILL WILL PROTRUDE A TINY BIT TOO MUCH ? ? ?
Rather than trimming the blank to length SOLELY by using your lathe and lathe cutting tools, you can get the blank trimmed down to an almost perfect length by doing the LAST BIT OF LENGTH TRIMMING ON A SHEET OF FLAT SANDPAPER and proceeding very carefully and very slowly so as to match the length of the pen blank to the length of the glued-in brass tube . . . . for the example under consideration here.
PLEASE UNDERSTAND ME . . . I am not trying to be harsh. I am merely trying to point out that there are often several different ways to proceed to your desired goal. You need to think about and keep in mind the alternative methods that are at your disposal.
It often takes a great deal of experience to keep EVERYTHING in mind ALL THE TIME.
ALL OF US ARE CONTINUING TO LEARN . . . ALL THE TIME. . . . and, embarrassing as it is to admit, we ALL MAKE MISTAKES . . . often by forgetting little things that we had previously known about.
EACH KIT PRESENTS ITS OWN CHALLENGES and we must always bear in mind the differences between kits, even though they look alike.
Being an OCD perfectionist is a good quality . . . if not an ESSENTIAL quality . . . when making pens, especially pens from different kits.
And do pay attention to the differences between the kits you use even though they may look very similar.
The length of the brass tube in a pen kit is one of most important dimensions that you must respect and maintain.
It controls the appearance and functionality of your pen.