Alec spent all episodes of 3B reassuring Magnus: of his worth, of his love for him, of his place on his side - but Magnus couldn't hear him. He wanted to, he wanted it to be true, but he didn't feel it for himself - nobody (even unending love and support) can make you feel whole but yourself.
So how should Alec who is no stranger to depression and self-worth problems understand what he means to Magnus if he is never explictly told? Even if Magnus really tried to explain that this love is special again and again he would need time to really feel it, but they never got around to this more complex aspect of Magnus' love, because of everything going on and just no time to find some peace to explore their love instead of always fighting for it.