Facepunch HUD elements are generally anchored to the screen corners, screen center, or screen edge midpoints, and then offsets are used from those. In my own CUI code, setting anchormin=anchormax to one of these 9 locations and then using offsets consistently allows me to align stuff with vanilla HUD elements - even when messing with the in-game UI scale slider.
Unfortunately Magic Panel uses anchors for everything, which breaks horribly if you touch the UI scale slider. Anchor-only alignment makes sense for menus but is extremely problematic for HUDs.