In case somebody else comes across this looking for a solution, here's a script that sets all the bones' scale to 1,1,1 in the selected armature.

#Set bones scale to 1
import bpy
from mathutils import Vector, Quaternion

arm = bpy.context.object

for pb in arm.pose.bones:
    pb.scale = Vector( (1, 1, 1) )

I don't think this is an intended behavior, or at least it shouldn't be. Bendy bone settings could be used as permanent effect, adding a bit of elasticity to cartoon characters. Having the Clear Transform option, which is often used for posing, clear those settings is very inconvenient. Took me a month or so after I started implementing bendy bones on my characters to notice why the Ease in/out settings kept getting reset, and it ended up being because I often select all bones and use Clear all transform to quickly get it back to T-pose.

Short description of error: In Pose Mode, when clearing any bones' Scale Transform, via shortcut Alt-S that bones' Bendy Bones' properties of Scale and Easing are reset to 1.0 and 0.0 respectively. This makes it hard to reset the whole armature easily, as each individual Bendy Bones' scale values X Y and Z have to be set to scale of 1 individually.

Oh trust me. this error goes as far as everything that has to do with Bendy Bones parameters. Action constraints literally cannot be used because of a similar issue. Also You would think you could add bone drivers to the parameters of the "stretch to" part of the bendy bone. Nope. Even the bones driving the parameter are bugged out.

Tested 12/12/2019 Blender 2.81**

I've added this issue to my Animation: Weak Areas wiki page, so that it's not forgotten.

Appreciated!