How to use safe center with flexbox?

The safe keyword is still a working draft, and not many (if any) browsers support it yet, so to get the same effect, cross browser, use auto margins for now, which should be set on the flex item.

Updated codepen

Note, to compensate for the modal's 50px top/bottom margin, use padding on modal-container.

.modal-container
{
  display: flex;
  flex-direction: row;
  justify-content: center;
  align-items: flex-start;                /*  changed  */
  position: fixed;
  width: 100vw;
  height: 100vh;
  overflow-y: scroll;
  padding: 50px 0;                        /*  added  */
  box-sizing: border-box;                 /*  added  */
}
.modal-container > #modal
{
  display: flex;
  flex-direction: column;
  align-items: center;
  margin: auto 0;                         /*  changed  */
  padding: 12px;
  width: 50%;
  background-color: #333;
  cursor: pointer;
}