Вы можете использовать array_walk:
$data = [
"Seccion 1 Pregunta 1" => [
"satisfactory" => 2,
"unsatisfactory" => 0,
"total" => 2
],
"Seccion 1 Pregunta 2" => [
"satisfactory" => 2,
"unsatisfactory" => 0,
"total" => 2
],
"Seccion 1 pregunta 3" => [
"satisfactory" => 0,
"unsatisfactory" => 1,
"total" => 1
],
"Seccion 2 pregunta 1" => [
"satisfactory" => 3,
"unsatisfactory" => 0,
"total" => 3
],
"Seccion 2 pregunta 2" => [
"satisfactory" => 1,
"unsatisfactory" => 1,
"total" => 2
],
"Commentarios seccion 2" => [
"satisfactory" => 0,
"unsatisfactory" => 0,
"total" => 0
]
];
$total = array('satisfactory' => 0, 'unsatisfactory' => 0, 'total' => 0);
array_walk($data, function($v) use (&$total) {
$total['satisfactory'] += $v['satisfactory'];
$total['unsatisfactory'] += $v['unsatisfactory'];
$total['total'] += $v['total'];
});