Okay, so, let me make sure I have this straight.

Captain Gavrilovich explores a planet, likes it, and decides he wants to start a mining colony. He first completes an Endeavor with his GM based around finding people and materials for this colony- presumably visiting Admech shipping yards for parts and technitions, and bartering with mining cartel lords and so forth.

Once it's time to start the colony, he rolls for profit factor cost, which for mining colony is 1d5+5 and gets a total of 7. His profit factor then decreases from 40 to 33, because he just spent seven PF to start a colony.

Mining Colonies have a starting statline of Size 1, Comp 1, Prod 2, Order 1, Pie 1. However, he immediately sets it to mine the Iron deposits he noticed when he was exploring the world. This gives it +2 productivity. At this point, the productivity is 4, which is greater than its size of 1, so the colony is now Productive.

A Size 1 Colony has a Profit Factor Value of 1, but a Productive colony gets +2, so the current PFV of the colony is 3. The good Captain now has a functional Profit Factor of 46, because Profit Factor Value is counted as part of your Profit Factor.

90 days pass. The Captain returns from his adventures to find a huge load of iron waiting for him. He takes it from the populace for a cool 3 Profit Factor. He succeeds on his Fellowship test, so complacency does not change. The colonists then roll 1d10 to see if they grow, and roll a 10! The colony grows. At this point, the GM rolls to see what infrastructure is required, and decides that Transport is needed. Complacency drops by 1, reaching zero! Order and Productivity now also decrease by 1d5, causing productivity to go down to 3, and Order to 0! The colony is now in open riots???

The Captain orders highways built. The colony gains +1 complacency for building new infrastructure, and +1 for transportation in particular. Order is still at zero. Fortunately, the Captain has ties with the Adeptus Arbites, and manages to call some in to quell the riots and establish an Arbites Precinct. +1 Order. Finally, he replaces the local mayor with his faithful Explorator with 60 int, as that player wanted to roll a psyker. This gives +2 to PFV. This gives the colony a total PFV of 4, which means the Captain is now up to 47 Profit Factor.

This cycle will repeat until the Colony becomes a Hive, at which point it may well have exhausted all local resources, but that's OK, because just owning a Hive is worth 18 PF.

So, current questions:

Is it intended behavior that most colonies will descend into chaos the first time they grow?

Taking all the resources for yourself has a chance to reduce Complacency by 1d5. The only way to raise this is by completing the Trappings endeavor, which means that every time the colony gets miffed, the Rogue Trader is obliged to go out and strangle 1d5 genestealers with his bare hands so he can cheer the population up with their skulls? It seems odd that qualities permanently decrease by so much.

So, it's apparently a very viable option to just grow your colonies, as that'll turn 7ish PF into 18 PF fairly quickly if you let them keep all their resources?