Hello, can i apply for visa to main land and hong kong at same time?

hi, i am iranian and i have my own company in Dubai and i have UAE residence visa
i do have 2 previous ones in past 2 years and i have 4-5 ones to Shengen and 2 UK in past 4-5 years.
can i apply for those to Hong Kong and Main Land at same time? how long does it take? do you keep passport during this period since i may need to travel in that period
thanks