Engineers say the Thompson Lykes damage is consistent with striking a "hull down" sub aft of the conning tower & slightly riding over the aft deck.

Surcouf was in radio silence but often disregarded this ie when escorting a convoy.

The bright flash seen by the ship's crew was most likely her main gun ammo (or torpedoes) exploding, causing flooding & her loss. Safety was not a priority aboard her & any unsecured shells would roll around in the accident.

She had gone out of control many times when diving & still recovered from below maximum depth - usually spilling the acid from her batteries (chlorine gas). Perhaps a "dead" boat may still contain enough air to float semi-submerged to the last position only then to be bombed by the USAAF.

You must remember that her crew were mostly untrained, some never having been to sea before joining Surcouf.