This is a mix from UNA Themes , maybe can help also over this.
1-I just create the first icon, the one you see "People" wich is not in same line. All other icons are the defaults from Protean. Just changed the new icon from default one in studio navigation options over this menu.
3- Did you also use code to align the icons yourself instead of Studio? --> Nope, i did not touch code in any moment, just tryng to upload differents icons sizes but alwais broke the line and unable to make this looks ok.