To scale X and Y at the same time using the Scale tool, don't use the handles. Just select the bone you want to scale, then click drag anywhere in the viewport away from the handles (the green and red arrows or shapes).
Spine's primary transform tools (scale, rotate, translate, skew) are designed to be used without needing to hit the handles. But you can use the handles in case you want to perform the transformations in specific ways.
For numeric input, yeah. Currently, you have to enter both.
. 5 tab . 5 enter is enough for that case.
