I agree with you
As I understand it, the User Startup is there to edit by hand if you want/need to. The Startup Sequence is then to be left alone and only to be edited 'automatically' by softwareinstallation programs and such.
But, imo, if you are capable enough to edit the User Startup, you are also capable of editing the Startup Sequence, thus leaving the division of startupfiles into two parts rather useles (I never understood why there was both a config.sys and an autoexec.bat in DOS).
So I've also removed my User Startup. Works for me...