31/31, 100%, Проверьте, пожалуйста

.palette-box:first-child .palette-small:first-child {
display: flex;
flex-direction: column;
justify-content: center;
}

.palette-box:first-child .color-2 {
order: 3;
}

.palette-box:first-child .color-3 {
order: 1;
align-self: center;
}

.palette-box:first-child .color-4 {
order: 4;
align-self: center;
}

.palette-box:first-child .color-5 {
order: 2;
}

.palette-box:nth-child(2) .palette-small:first-child {
display: flex;
flex-direction: column-reverse;
justify-content: space-between;
}

.palette-box:nth-child(2) .color-2,
.palette-box:nth-child(2) .color-6 {
align-self: flex-end;

}

.palette-box:nth-child(2) .color-4,
.palette-box:nth-child(2) .color-1 {
align-self: flex-start;
}

.palette-box:nth-child(3) .palette-small {
display: flex;
}

.palette-box:nth-child(3) .part:first-child {
display:flex;
flex-direction: column;
}

.palette-box:nth-child(3) .part:last-child {
display: flex;
margin-left: auto;
flex-direction: column;
}

.palette-box:nth-child(3) .color-3,
.palette-box:nth-child(3) .color-6 {
margin-top: auto;
}

.palette-box:nth-child(4) .palette-small,
.palette-box:nth-child(4) .part:first-child{
display: flex;
}

.palette-box:nth-child(4) .part:last-child {
display: flex;
flex-direction: column-reverse;
margin-left: auto;
}

.palette-box:nth-child(4) .color-3 {
margin-bottom: auto;
}

Если интересно, как ещё можно сделать:

Чуть короче
.palette-small,
.part {
    display: flex;    
    align-content: space-between;
}

/*первый квадрат*/
.palette-box:nth-child(1) .palette-small {
    flex-direction: column-reverse;    
    justify-content: center;
}
.palette-box:nth-child(1) .color-4 {
    order: -1;
    align-self: center;
}
.palette-box:nth-child(1) .color-3 {
    order: 1;
    align-self: center;
}

/*второй квадрат*/
.palette-box:nth-child(2) .palette-small {
    flex-direction: column-reverse;    
    justify-content: space-between;
    align-items: flex-start;
}

.palette-box:nth-child(2) .color-2,
.palette-box:nth-child(2) .color-6 {
    align-self: flex-end;
}

.palette-box:nth-child(3) .palette-small,
.palette-box:nth-child(4) .palette-small {
  justify-content: space-between;
}
/*третий квадрат*/
.palette-box:nth-child(3) .part{
  flex-direction: column;
  justify-content: space-between;
}

/*четвёртый квадрат*/
.palette-box:nth-child(4) .part:last-child {
  flex-direction: column-reverse;
  justify-content: space-between;
}
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