The thing is that the spire story line is harder then the base game as are the other win conditions, and succeeding the shard returns is actually really hard without enough territory conquest.
Which is fine, since the Fallen Spire mode is designed as a more conquest oriented game-mode.
Also also it's one of those things that can be gamed super hard, say for example by carefully choosing a perfect x map or maze map to really minimize the number of planets needed to be taken and then save/loading the shard locations in conquered systems.
Which is also fine, since players are not competing against each other. Instead, each player chooses whatever setup he thinks will entertain or challenge himself when fighting the AI. Want an easy game, choose an easy map. Want an even easier game, use save and reloading liberally.
And now that I've played building cities on nomads I had lots of fun but still needed to take territory to succeed the spire storyline since otherwise I would have had to save/reload really hard to win and I don't enjoy that. Overall I felt that I would likely turn on and use spire more often if it was always like this, with higher risk/rewards possibities, I'd at least like to give it a try.
A much more interesting argument.
I like the current approach because it makes the distinction between level 1 and level 2 spire cities meaningful: You cannot create chokepoints for regular AI waves that have level 2 spire cities. That makes expansion and site selection for spire cities trickier.
On the other hand, I can also see how your idea could be fun - but it surely would make Fallen Spire considerably easier overall.
That's not necessarily a problem, but it might be a consideration.
