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Found the culprit and it has nothing to do with the test framework: Magento\CatalogSearch\Model\Indexer\Fulltext\Plugin which adds commit callbacks for saving and deleting products.

If an exception is thrown in a commit callback, rollback() is called additionally to commit()

private function addCommitCallback(ResourceProduct $productResource, \Closure $proceed, AbstractModel $product)
{
    try {
        $productResource->beginTransaction();
        $result = $proceed($product);
        $productResource->addCommitCallback(function () use ($product) {
            $this->reindexRow($product->getEntityId());
        });
        $productResource->commit();
    } catch (\Exception $e) {
        $productResource->rollBack();
        throw $e;
    }

    return $result;
}

In Magento\Framework\Model\ResourceModel\AbstractResource, exceptions from the commit callbacks are simply rethrown:

public function commit()
{
    $this->getConnection()->commit();
    /**
     * Process after commit callbacks
     */
    if ($this->getConnection()->getTransactionLevel() === 0) {
        $callbacks = CallbackPool::get(spl_object_hash($this->getConnection()));
        try {
            foreach ($callbacks as $callback) {
                call_user_func($callback);
            }
        } catch (\Exception $e) {
            throw $e;
        }
    }
    return $this;
}

The two methods together lead to this nasty bug. To fix it, either exceptions from commit() or exceptions from the callbacks should probably be wrapped into a different exception type that can be handled differently by the core plugin.

Until this is fixed, "just" make sure that commit callbacks never throw exceptions...