No, the timing marks shouldn't be there. The reference mark on the rotor looks correct, at about the 5 o'clock position from the magnet if the magnet is at 12 o'clock .....
View attachment 335425
That leaves only the keyway and/or mounting. Maybe the keyway was machined in the wrong spot, or the rotor was mounted without the key in there.
As far as the reg-rec issues go, I'd say your new combined unit is bad. It's not uncommon. Most of those units are cheap, Chinese junk, even though they can cost quite a bit. Many of us "roll our own", so to speak, using an automotive regulator and a rectifier from the electronics world. Much cheaper and more reliable ......
https://www.xs650.com/threads/diy-reg-rec-5twins-and-jim.55842/