I need to know for sure, if the missing custom font which was used in PPT will be changed to Calibri, not something else?
Also, aren't there yet an option to embed the custom font in PPT?
Harrymc's answer is correct if the custom font has embedding enabled. The font's author can choose to allow embedding or not. If not, then PowerPoint won't embed the font.
PowerPoint (or Windows, I'm not sure at what level this happens) uses a system called Panose to choose the installed font that's closest to the missing font. It won't always choose Calibri.
You don't have to guess, you can Embed fonts in Word or PowerPoint:
In the File tab click Options
Select the Save tab
Under Preserve fidelity when sharing this presentation select Embed fonts in the file
There are other options that you may select if needed: