Clearly the specs for the R8 collet are well known and published by Bridgeport, Hardinge and no doubt multiple other manufactures of premium collets. The spec. for the R8 collet OD limit is 0.9495", the degree that a collet producer adheres to this spec, their tolerance limits, and their QC varies by manufacture. On Hardinge R8 collets the spec. is +0.0000 -0.0003. When I measured my Lyndex and Royal (Crawford) R8 collets they were all 0.9495 or slightly under. The spindle ID is manufacturer specific. If your collets meet this spec. and the spindle did not fit it, then clearly the spindle was faulty and should have been replaced under warranty. If you now feel that the spindle OD is bored concentrically and too the proper dimension then end of story. I have yet to see that you evaluated any axial deviation measurement at say 3-4" from the collet with an accurate test gauge. I can assure you that you need a gauge that can measure down to 0.0001" to have any meaningful results. Repeat the test pulling the drawbar up and down several times. If they are reproducible then you are should be OK as too the vertical collet alignment in the static mode.
View attachment 303846
Given that the R8 collets has been around for a long time requirements for manufacturing are quite tight, I seriously doubt the it is just haphazardly decided as to what the spindle bore should be and that the upper dimension can be whatever they decide on that day. If this was the case the surfaces would not be precisely ground to interface with the corresponding spindle interface. I have had no "zero" issues with quality collets and arbors AND have only had issues with generic collets like the Interstate for whatever reason. Other problems I have seen is the guide pin is set too deep (or is too wide) or the threaded portion of some arbors is not deep enough preventing the drawbar from not being able to pull the collet completely vertically.
If you look at other similar collets like the 5C, the rear ground surface is precisely ground despite being pulled back by a threaded portion similar to the R8, any small deviation in axial play results in measurable skew. The back interface on my Bison 5C chuck is very tight, previous Chinese chucks less so and it showed more inconsistency in axial deviation. There are also limitations to R8 system because of the nature of the collapsible interface of collets as compared to other collet systems/spindle interfaces which offer far better concentricity and rigidity.
The R8 drawbar is not precisely located and it is made to pull up on the collet, and not provide a lateral position of the collet. In my mill it rattled around until I modified the spacers. A small deviation at the top of the collet when the collet is drawn up of say 0.001" would result in a corresponding runout/wobble at the cutter tip. When milling there are vibration/oscillating forces, with corresponding movement/deflections at the end mill tip. The forces and effects can only be determined in a dynamic situation and is specific to the cutter type, collet, clearances, rigidity, etc. It is a known fact that runout of endmills corresponds to endmill life in a production environment, as well as the accuracy of the finished product. Clearly these are not issues in your situation.