How do I make sure manual ISO and Exposure are exactly as I wish?

When you want your final photo to have ISO and exposure time exactly as dialed in, please disable SmartHDR (the HDR button on the viewfinder).
 
SmartHDR comes with (deep) fusion, and that is automatic in regards to best exposure times and ISO. The final picture should always look like it does in the viewfinder - even if the camera chooses different ISO and exposure time.
 
For actual manual exposure, everything that is “smart” needs to be disabled, hence please disable HDR on the viewfinder.
Please note: this only works in M/SI-Mode. In A-Mode SmartHDR is always enabled.
 
For general information on manual controls, check out Manual controls in ProCamera article:

Manual controls in ProCamera