Yes you can do that with Litchi. In Litchi, set up your C1 or C2 key to “set waypoint”. Then when you want to set a waypoint, just press that key. I think there are videos on the internet which can further guide you. It has been a while since I have done this.
I have used this option several times and it works really well. Just remember when you've completed marking your waypoints, to save the mission. Speaking from experience, it will save you time and frustration of having to start all over.
Maven app has an 'In Flight' mission, with which you can add waypoints as you go. Very useful in that you can make a tricky flight, such as flying through a window or under a low bridge, slowly and carefully. Save the mission, edit it at your leisure, then fly it again, fast and cinematically smooth. Very professional looking...
I create waypoint missions all the time during flight (M2P) in the "Go app"
It is also easier especially when using a phone as opposed to a pad of some kind. And as stated earlier, be sure to save the mission in the app. You can always edit the mission later to make adjustments and tweaks.
Fly Safe!