I can only help you with the last 3 questions, as I have never had to pay Quellensteurer.

4) No this is not usual. I just checked a few of my salary receipts. I had a 13th salary (paid 50% june, 50% december), plus a monthly performance bonus. Each month all INCOME was added together, and then AHV, ALV and PK deducted on this amount.
I believe their is an employer contribution to your private pension fund. I would say if they are deductiong PK at 48000, they are doing so to reduce their contribution. I doubt it is legal.

5) Tax alone can be up to around 25% of gross income, with Health insurance 31% is not unusual.

6) Quellensteuer is deducted per month on that monthly income, as if you were paid this amount every month. Therefore, if you are paid your 13th everymonth pro rata, you probably pay a little less tax than someone who gets it lump sum at the end of the year. A 13th is equally taxable as the other 12 months.