Short Answer
If you do not want to display the scrollbar all the time, wrap your content into <div> elements etc. you can use JavaScript to add a certain value to all media queries when the scrollbar is shown.
// check whether scrollbar is visible
var isScrollbarVisible = window.innerWidth > document.documentElement.clientWidth;
// search for media rule
var mediaRule = document.styleSheets[i].cssRules[j];
// update media rule
mediaRule.media.mediaText = '..'
Long Answer
I wrote a small script which you can include on your page. It detects when the window is resized and changes all media queries if needed. The value of the css variable --replace-media-scrollbar is used as the width of the scrollbar or 15px if no value was found. This works for the media queries with, min-width, max-width, height, min-height and max-height even when they are connected using and.
JavaScript:
function* visitCssRule(cssRule) {
    // visit imported stylesheet
    if (cssRule.type == cssRule.IMPORT_RULE)
        yield* visitStyleSheet(cssRule.styleSheet);
    // yield media rule
    if (cssRule.type == cssRule.MEDIA_RULE)
        yield cssRule;
}
function* visitStyleSheet(styleSheet) {
    try {
        // visit every rule in the stylesheet
        var cssRules = styleSheet.cssRules;
        for (var i = 0, cssRule; cssRule = cssRules[i]; i++)
            yield* visitCssRule(cssRule);
    } catch (ignored) {}
}
function* findAllMediaRules() {
    // visit all stylesheets
    var styleSheets = document.styleSheets;
    for (var i = 0, styleSheet; styleSheet = styleSheets[i]; i++)
        yield* visitStyleSheet(styleSheet);
}
// collect all media rules
const mediaRules = Array.from(findAllMediaRules());
// read scrollbar width
var style = getComputedStyle(document.documentElement);
var scrollbar = style.getPropertyValue('--replace-media-scrollbar') || '15px';
// update media rules
if (scrollbar != '0px') {
    var oldValue = '0px';
    function updateMediaRulesScrollbar() {
        var newValue = window.innerWidth > document.documentElement.clientWidth ? scrollbar : '0px';
        // if value changed
        if (oldValue != newValue) {
            for (var i = 0, mediaRule; mediaRule = mediaRules[i]; i++) {
                var regex = RegExp('\\((width|min-width|max-width|height|min-height|max-height): (calc\\([^)]*\\)|[^)]*)\\)', 'g');
                var replacement = '($1: calc($2 - ' + oldValue + ' + ' + newValue + '))';
                mediaRule.media.mediaText = mediaRule.media.mediaText.replace(regex, replacement);
                console.log(mediaRule);
            }
        }
        oldValue = newValue;
    }
    updateMediaRulesScrollbar();
    window.onresize = updateMediaRulesScrollbar;
}
Optional CSS:
:root {
  --replace-media-scrollbar: 15px;
}