I have an update to this question. So, it is related to the smooth gearing at the end, but not directly as it would be if the secondary chain was also timed in a similar way as well.
What happens is the crankshaft and the secondary shaft must be balanced for smooth transition of power, and the chain acts as a balancer once both are timed correctly. The secondary shaft needs to be positioned (timed) correctly in relation to where the pistons are. Not being balanced would also affect the gear changes. But that's not the biggest problem but rather an aftereffect. Without being balanced correctly, the engine would shake and eventually fall apart. That's the real danger and the reason for timing them. When everything is smooth at the secondary shaft, all that's behind (the gearbox) will work smooth as well.
That is it, unless anyone has something to add.
Cheers!
Stan
The secondary shaft.