The Future Perfect Continuous can be also used to predict what was
happening in the past.
I don't think that predict is the best way to understand the construction being used here. To predict generally means to say what you think will happen in the future. But in the packing boxes and gardening examples there is no prediction about the future involved. Rather there is a supposition or assumption about the past.
Collins Cobuild English Grammar (p223) explains this particular use of will as follows:
You use 'will' when you are assuming that something is the case and
you do not think there is any reason to doubt it.
- Most listeners will have heard of hormones.
As an alternative to the use of will in your sentences, you could use the past continuous with probably (or as in the second case just leave the I expect to convey the probability):
What do you think the men were doing in the store room? - Don’t worry. They were probably unpacking boxes.
What do you think those men were doing in Charles's garden yesterday? I expect they were doing some gardening.