There may be a misunderstanding here...
Those metrics don't actually affect the glyph size, height or alignment at all. They're just meta data that aren't of much use in general usage. Specifically in Glyphs (which I can see your font info dialog is from) The x-height will control the display of the box in your glyph view.
This, for example, is the difference between a 600 x-height...

And a 300 x-height...

All that happened is that a guide line, that showed me the x-height has moved. The font will still render exactly the same as it did before and no one would be any the wiser.
The cap height set in your example is nonsensical and useless. Ignore it.
The metrics defined in the Custom Parameter section are metrics which do affect the rendering of your font in some applications*, but they affect the alignment and sizing of the font as a whole. There is no metric that will change the relative height of some glyphs compared to others (e.g. change the x-height or cap height without also changing every other metric).
* See https://glyphsapp.com/tutorials/vertical-metrics