In a practical sense, the only effect that Vortex's Mods tab has on plugins is determining which ones show up as installed, i.e., available to activate on the Plugins tab. Changing the order of the plugins on the Plugins tab will do nothing whatsoever to the Mods tab; they are completely separate entities.
I think, though (and this may be a linguistic issue), what you're asking is: does Vortex sort the mods on the Mods tab by whether they have a .bsa or not? No, it does not. Or at least, I haven't noticed an option to that effect yet. By default, it sorts your mods on that tab alphabetically by the first word of the mod name. While there is a column on the Mods tab named Install Order, it is hidden by default, and at least right now for me doesn't show anything anyway. Probably means that particular bit of code hasn't been implemented yet...
EDIT: After rereading that last post, I should probably clarify: The only way the sort on the Mods tab is going to change is if you do something manually to change it - pick a different sort such as name or status, etc., or install a new mod.
Edited by HardwareSc8, 13 February 2018 - 06:08 PM.