The crafting essentially has you saving some gold at the expense of total exp:

L5 Manyu = 720 exp
L20 Manyu = 1800 exp
L100 Manyu = 4800 exp

3 L5 Manyus: 1 L20 Manyu is a loss of 360 exp.
3 L20 Manyu: 1 L100 Manyu is a loss of 600 exp.

But, it costs less gold to fuse one Manyu compared to three of them; if gold isn't an issue, then the only other purpose would be to consolidate for storage. Sure, the crafting will be a QoL change, but it doesn't seem to be that huge of a deal to me.