Sforno on Genesis 49:28/ספורנו על בראשית מ״ט:כ״ח

1כל אלה שבטי ישראל, the ones Yaakov mentioned here were the true twelve tribes of Israel, the names inscribed on the breastplate of the High Priest as commended to G’d’s special attention. They are also the ones who were mentioned as such at the covenant on Mount Gerizim and Mount Eyval. The twelve stones which Moses erected also symbolised these twelve tribes. Again. Joshua erected 12 stones at the Jordan as well as at Gilgal, and Elijah erected 12 stones at the altar. In none of these instances are Ephrayim and Menashe treated as separate tribes. They only figured as separate tribes when it came to the land distribution, seeing that the tribe of Levi did not share in that.

2ויברך אותם, in addition to blessings bestowed individually rather than collectively, earlier.

3איש אשר כברכתו ברך אותם, he gave an individual blessing to each one in accordance with what he perceived to be the son’s need in view of his eventual destiny. Yehudah needed to have a blessing that his dynasty would endure, etc. Levi needed to be blessed that his function of serving G’d as representative of the people would endure, etc.