Well, yeah, that's possible.
If you think about it, that's close to what a power grid is – a lot of different power sources feeding one network.
Luckily, this works on smaller scales, too, and slightly easier, without having to operate all the power plants synchronously:
In a DC network, you'd "agree" on a fixed voltage, like you'd suggested. Typically, you'd even buffer that voltage with very "agile" power storages – in your dimensions, large capacitors, probably – and feed the load from that.
Now, the question is which voltage to agree on. Intuitively, yes, stepping up the 9 V to 12 V would allow you to directly cooperate with the 12 V source and feed the 12 V load.
That works well if the 12 V load isn't very sensitive to slight voltage variations – because there's little to no "headroom" for the power sources to cooperate in case of a load increase.
So, if your 12 V load isn't very sensitive, or you can significantly overdimension your boost converter to handle a load increase e.g. from 10 W to 50 W without dropping much on the 12 V output, then go directly.
In many cases, but that really depends on the characteristics of your power sources and loads, to have the multi-source voltage (let's call it intermediate circuit) "far enough" from the output voltage to allow for an effective SMPS to react to a changing sources voltage without significant effect on the load voltage.