Possible Opacity Z-Index Bug

What has bigger priority: opacity or z-index in browsers?

This is not a bug and is actually how it's supposed to work. It's a bit confusing as the elaborate description of Stacking Contexts doesn't mention anything about it. However, the visual formatting module links to the color module where this particular gotcha can be found (emphasis mine):

Since an element with opacity less than 1 is composited from a single
offscreen image, content outside of it cannot be layered in z-order
between pieces of content inside of it. For the same reason,
implementations must create a new stacking context for any element
with opacity less than 1. If an element with opacity less than 1 is
not positioned, implementations must paint the layer it creates,
within its parent stacking context, at the same stacking order that
would be used if it were a positioned element with ‘z-index: 0’ and
‘opacity: 1’. If an element with opacity less than 1 is positioned,
the ‘z-index’ property applies as described in [CSS21], except that
‘auto’ is treated as ‘0’ since a new stacking context is always
created. See section 9.9 and Appendix E of [CSS21] for more
information on stacking contexts. The rules in this paragraph do not
apply to SVG elements, since SVG has its own rendering model ([SVG11],
Chapter 3).

Possible Opacity Z-Index Bug

This issue is already known.
https://www.google.com/#q=opacity%20change%20z-index

You should use rgba background, which is also a widely supported property.

Z-Index and Opacity not working as expected

If the issue is just that the buttons and things overlap the top header when you scroll, simply put a high z-index on the #top element. E.g.

#top {
    z-index: 1000;
}

How to fix a z-index issue in Bootstrap?

please update your css like this

/*----------ESTILOS MENU -----------*/
      .menuBtn {
        height: 30px;
        width: 30px;
        position: absolute;
        right: 20px;
        top: 10px;
        z-index: 101;
      }
      .menuBtn > span {
        background-color: var(--color-primario);
        height: var(--altura-linea);
        width: 100%;
        position: absolute;
        left: 50%;
        top: 50%;
        margin: -1px 0 0 -15px;
        transition: height 100ms;
      }
      .menuBtn > span:after,
      .menuBtn > span:before {
        content: '';
        background-color: var(--color-primario);
        height: var(--altura-linea);
        width: 100%;
        position: absolute;
        left: 50%;
        margin-left: -15px;
        transition: all 200ms;
      }
      .menuBtn > span:after {
        top: -7px;
      }
      .menuBtn > span:before {
        bottom: -7px;
      }
      .menuBtn.act > span {
        height: 0;
      }
      .menuBtn.act > span:after,
      .menuBtn.act > span:before {
        background-color: #008877;
        top: 1px;
      }
      .menuBtn.act > span:after {
        transform: rotate(45deg);
      }
      .menuBtn.act > span:before {
        transform: rotate(-45deg);
      }
      /* main menu block */
      .mainMenu {
        background-color: var(--color-blanco);
        position: fixed;
        left: 0;
        top: 0;
        z-index: 100;
        height: 100%;
        width: 100%;
        display: table;
        text-align: center;
        opacity: 0;
        transition: all 500ms cubic-bezier(0.68, -0.55, 0.265, 1.55);
        transform: scale(0);
      }
      .mainMenu.act {
        opacity: 1;
        transform: scale(1);
      }
      .mainMenu.act ul li {
        opacity: 1;
        transform: translateX(0);
      }
      .mainMenu ul {
        display: table-cell;
        vertical-align: middle;
      }
      .mainMenu li {
        padding: 8px 0;
        transition: all 400ms 510ms;
        opacity: 0;
      }
      .mainMenu li:nth-child(odd) {
        transform: translateX(30%);
      }
      .mainMenu li:nth-child(even) {
        transform: translateX(-30%);
      }
      .mainMenu li:last-child {
        transform: none;
      }
      .mainMenu a {
        color: #19b698;
        display: inline-block;
        font-size: 18px;
      }
      .mainMenu a.suBtn {
        color: var(--color-blanco);
      }
    
      .act{
        background-color: red;
      }

Div, z-index, opacity. Bug, feature or user relate issue?

Your problem is with an unexpected stacking context being established by #menu.

To quote MDN:

A stacking context is formed, anywhere in the document, by any element
which is either

• the root element (HTML),
• positioned (absolutely or relatively) with a z-index value other than "auto",
• elements with an opacity value less than 1.

This is the reason your div is behaving unexpectedly when you apply an opacity < 1 to it. #menu now establishes a separate stacking context, and the z-index of its descendant #status has no meaning outside of this context. To correct this problem, apply the z-index to #menu itself.

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