STV is not proportional - it's still winner takes all: just that "winner" has to have the approval of at least half the voters (on 2nd and subsequent preferences if necessary).
The d'Hondt system apportions seats in an approximately proportional way, but has to handle the fact that you can't have a fractional seat. The larger the number of seats, the more proportional it gets. Compare the North East, where Brexit got two of the three seats on less than 40% of the vote, with the South East where they got four of the ten seats on 36% of the vote). (In a hypothetical single-seat constituency it reduces to "First Past The Post".
What happened in the East Midlands is that no party other than those that won seats got more than 11% of the vote. (Conservative 10.7%, Green 10.6% - Brexit scored more than three times that). It would have been just as disproportionate for either of those to get one of the five seats available. (In fact 13% would have been enough to take the fifth seat).