" set(obj.Panel,'Parent',obj.Parent)
however I am worried that this might cause bugs in the future"
You're absolutely right. This is not a good idea.
Your problem is that the panel's default units are "normalized" so setting anything outside the bounds of 0 and 1 results in something way off-screen (of the componentcontainer object). In your panel constructor call, set the units to pixels before setting the position property.
Better yet, I strongly encourage the use of uigridlayout. Every componentcontainer I build starts with a grid. Using grids makes nearly every conversation about size and position irrelevant. It also cures practically every situation such as this one - "what's wrong with my component positioning?".
