It\'s rather annoying and I can\'t seem to figure out why.

If you don't want to disable SublimeLinter completely, you can set Syntax Specific Preferences.
Preferences -> Package Settings -> Sublime Linter -> Settings Syntax Specific User
The preferences is evaluated similar to CSS, it cascades. Think about the most user-specific, syntax-specific rules evaluated last.
E.g: I also do not like the white rectangle, so I opted for fills.
{
/*
Selects the way the lines with errors or warnings are marked; "outline"
(default) draws outline boxes around the lines, "fill" fills the lines
with the outline color, and "none" disables all outline styles
(useful if "sublimelinter_gutter_marks" is set).
*/
"sublimelinter_mark_style" : "fill",
/*
If true, lines with errors or warnings will be filled in with the
outline color.
This setting is DEPRECATED and will be ignored in future
versions. Use "sublimelinter_mark_style" instead. For backwards
compatibility reasons, this setting overrides "sublimelinter_mark_style"
if that one is set to "outline", but has no effect if it's set to "none".
*/
"sublimelinter_fill_outlines": false,
// If true, lines with errors or warnings will have a gutter mark.
"sublimelinter_gutter_marks": false,
// If true, the find next/previous error commands will wrap.
"sublimelinter_wrap_find": false,
}