I;ve always felt that font sizes in the text module displayed bigger than should be but was not quite sure. However I have created the same section - one as a Heading and the second in a text module - bit the size is displayed differently. The text module seems to display the size larger when using TinyMCE Advanced Font sizes in the text module or when using HTML to change font size in text mode.
Thanks for getting in touch. The WordPress editor or tinyMCE uses pt values as default for their font-sizes. If you take a look at your 2nd screenshot, the font-size is 46pt whereas on the 1st screenshot, it is 46px. You can manually change the value to 46px on the text editor and that should take care of it. You can also check out this thread to try and change the default values.