If you run file I uploaded and set depth of cut in last setup deeper then flute length, do you get same warning shown in screenshot of my post?
I mention leaving slightly more radial stock on each new depth pass to avoid shaft rubbing against walls of previous pass, this is not possible within same operation so to achieve that, I would have to duplicate operation several times and increase radial stock to leave by small value for each level.
This would have to be followed by contour, perhaps 2 passes, one to take out stairs and one final pass to finish size, using tool with full length of flutes.
Now if I was planning to run such job, advantage of using short flute tool would be that tool is stronger and can be driven faster then if I use full length of flutes to rough and finish.
In this scenario, I am planning exactly what to do and get result I expect, whether or not Fusion will detect something out of place and display warning is besides the point, some things are simply matter of doing what we do
knowing that outcome is within desired parameters.
Prime example of Fusion not being any help is when I use grooving tool as turning tool, normally Fusion will turn the tool red and display message saying tool is not compatible with operation, nonsense, if I can undercut grooves with turning tool, why can't I do minor turning with rigid grooving tool?
So, I can do turning with turning tool but later change that to use grooving tool instead, even "stupid" has practical workaround so warnings built into Fusion are what they are based on someone's perception of right and wrong, not necessarily in sink with actual case in point.