Yes this is true, the 35 Whelen has been plaqued by this minimal shoulder problem for a long time. In a Mauser with the claw extractor it is not noticable the extractor holds the case back. Neck sizing in a Mauser will cure this problem, but not in a Handi. Handi calibers need the shoulder adjusted/set back after each firing.
This is the reason why I thought the 35Whelen to be a poor Handi choice.
The primer below the case bottom is normal. I have a primer pocket uniformer tool that reams the bottom of the hole 0.130" deep. The primers I use are .126", so they will be four thou below the case bottom. The 4 thou will take care of any primer variation. Primers should not be crunched down, only seated to to a clean bottom.
Most head space gauges include up to 10Thou head space. Don't know what H&R uses for head space on the 35W. Now all you have to do is add a bit of gap to the barrel face and the hammer will drive the case forward some, and you will have a miss fire.
The best you can do is get your own cases, expand the neck to 375 and form a new shoulder with no head space, meaning the the case is flush with the barrel face. Then watch the cases and set the die so the base of the case is always flush when sized.
When I chambered my 257R and the 6x47 we used a new case for a gauge, no head space. If the case is stretched by the springy action, the die ist set to move the shoulder back to flush again. Of course I never use factory ammo so I don't know if the fit well.
Eventual the cases will seperate after asbout 8-9 reloads because of the stretching action. Some calibers in Handi's will will not stretch/spring back the action much but most do. Gung-Ho pressure and velocity is not recommended for this reason, besides it does very little for the effort.