Re: How Clean Is Clean
I've seen my mason bees chew through parchment paper to remove pieces of it that were 'in the way' inside the cardboard tubes. I'd say: if there are big woody bits, you'd want to remove those, but any little wispy shreds of papery pulp will be chewed off and removed by the bees. Make sure the entrance is not obstructed.
One thing i note is where you say you can 'see through the stalks'. That means there is no plugged end at the back? The nice thing about Japanese knotweed is that it has culms, or nodes, separating each span of open tube- just like bamboo grows:
When I cut my japanese knotweed, I leave one closed node for the back end of the tube and the entry end is left open by cutting the node off on that end. Thus, you can take advantage the closed culm end to keep predators like wasps or beetles from gaining access into the back end of your nesting tube. It's one of the cool features of knotweed. Remember, the females are usually cocooned at the back end, so it's especially desirable to protect that end. The males at the open front end are more expendable and losing one or two of them is not the end of the world.
All that said, I should mention that I put out a big can with J.knotweed tubes of various sizes last Summer and no bees have shown interest in it yet, despite have dozens of females nesting my cans of cardboard tubes. It's still there in my garden waiting for tenants, so if no one nests in it by this Summer I'll take it down.
Hope this helps!
Here's a photo showing bamboo tubes used for mason bees. Notice how the node is left on the back end to keep the tube safely closed and protected there:
The little bee returns with evening's gloom,
To join her comrades in the braided hive... -Tennyson