The difference between free-flow and intensive immersion is that free-flow is more passive and relaxed, while intensive immersion involves actively looking things up and making cards. During intensive immersion, it is expected that you make flashcards as you are already putting in the effort to look up words.
However, sentencing mining during free-flow immersion instead of intensive immersion is a viable option. If that is the method that works best for you, then go for it. But you'll have to rearrange the process of making your flashcards. When watching a movie, for example, you usually pause to look up an unknown word and then make a targeted sentence card with a chosen dictionary definition. But since free-flow immersion doesn't involve looking up words, when you come across a new word, you just make a card with the sentence. In MPV with mpvacious you can press one button to make a card. The key is not to interrupt the flow. Then, you would dedicate a period of time to go through the new flashcards and add dictionary definitions, mark the target words, and include other relevant information.
If making cards during free-flow immersion is more effective for you, there is no reason not to do it. I do it myself when I feel like it.