You are using a gage pin which is very close to the nominal diameter of the endmill holder but in my experience most carbide end mill shanks are .0004" to .0005" under nominal size which would make the endmill holder runout even worse but would have little to no effect on the ER holder. There is always some clearance between the endmill and bore of the holder on a set screw type holder, collet holders always center the end mill instead of pushing it against one wall of the bore basically giving you two points of contact. Thermal endmill holders are different but they're a more expensive investment and are more time consuming to set up.
these can be found at any industriual supply house. MSC and Mcmaster-Carr bot hcarry gage pins. The perpendicularity of the end face to the diameters is likely pretty good but i do not know who well it is controlled. you would want to buy and measure.
in any cenario you can allways grind your holder inside your machine 0 runout. ever ER holders. even holder is acurate. collets is moving part. runout change on life time and how you insert it buy closest inch or mm holder and grind it your desire size. you decide how tight it is. when it BLOB its good :)
EM holders are very unbalanced especially if you grind the flat yourself, and if an EM shank is way undersized, the run out will increase accordingly. ER collet chuck, though your video shows it gives a tenth run out, everyone who uses ER knows, you don't get this every time, in fact, it takes an average 5-6 minutes to get an ER holder + collet to give less than 4 tenths run out (that means at the high range, one can takes up to 15 minutes to dial it in). Economy brand ERs also don't provide enough gripping force for aggressive milling. A brand X ER32 holder with a 1/2" collet gives any where from 35-50 ft bls of holding torque (LyndexNikken brand gives 110 - 125 ft lbs. and more consistency in run out - less than 5 tenths). If you want versatility - milling, drilling, tapping, reaming, etc... go for the Lyndexnikken premier SK collet chuck system. For a 1/2" shank, either their SK16 or SK20 can give more than 150 ft bls of gripping force and they guarantee run out of less than 2 tenths - every time. The SK system is awesome, I have used it for many years. Little more money up front but boy you will get back the investment in days just from the time saving and the longevity of the carbide. Many high end shops no longer use EM holders and some still use ER, but majority have switched to LyndexNikken SKs. Hope this helps, but do look into it though, you won't regret it.
SK holders are a bit extra money but its practically set it and forget it. with a run out of .0002 or .0004 max if you are unlucky. Only issue is the range, but man are they accurate
