Thing is, the Kaos DLC doesn’t have a timers for the mission, and you can only go there after you accept the challenge… aka you get to choose when you pick it up.
The balance issues aren’t a function of Phoenix Point being a sandbox type game. Harebrained Studios/Paradox’s 2018 Battletech game is a well balanced turn-based combat game with giant sandbox galaxy for the player to explore–along with a functional side-grade ecosystem.
BattleTech, like Phoenix Point, started as a kickstarter project, and in many ways are very similar games. BattleTech has official mod support and a thriving mod community. If Phoenix Point was balanced, it could have been the kind of commercial and critical success that BattleTech became.
What the developers did with BattleTech is create a skull-rating system for missions and then added a slight variance to that so that sometimes the player got a mission that was slightly easier than advertised. And sometimes it was tougher. But the player had the tools to make a reasonable assessment of whether a particular mission would be an appropriate challenge. One of the NPC characters would even warn the player about them being outgunned if they were going to take on a mission where they would most likely be outclassed. And if the player did that mission anyway and got wrecked, well, fair is fair, that’s on the player.
There is this fundamental awareness of players playing their game and some thought about ensuring that players have an enjoyable experience playing their games at other development studios. And that kind of thought, care, and awareness just appears to be completely lacking at Snapshot Games.
Snapshot has build a sandbox game that’s more like a cat litter box, and they seem to be a bit perplexed about a few people complaining about all the shit in it.
Likewise, many RPG games are open world, sandbox games. But there is a levelling system, and players can easily determine if their characters aren’t levelled up enough to tackle a certain part of the map.
Phoenix Point, on the other hand, just throws everything at the player all at once. And the only tools players have to structure the game appropriately are forums and posts on social media where they can find advice from more experienced players about the meta for the game.
The irony of Phoenix Point is that you get this open world sandbox game with an increasingly rigid meta about what missions to do first and what missions ought to be delayed until later.
As for mission design, that definitely needs an overhaul–especially the Nest, Lair, and Citadel missions. Nests still have the old, pre-alpha insta-win when the second giant mushroom is taken out. And for some weird reason, we have to evacuate from Lairs and Citadels. Plus on some Citadel missions, there is massive design flaw that allows screaming towers to be placed on the other side of a tall wall next to the players starting position. If the developers are going for the OG XCom vibe where the player’s squad is gunned down as they step off the transport, well, the succeeded here because the screaming tower triggers on the player’s first move, and the player will need a few turns just to get to that towers, so they are going to lose 8 willpower per turn from the tower and be down -24 willpower in no time, more if they actually use soldier abilities. And, yes, I know that 20 willpower is the maximum–with a few soldiers being able to reach 24 with the right random perks. On Legend difficulty with early game squads, that mission layout is a recipe for a squad wipe. Soldiers will be locked down in panic mode quickly while infinite reinforcements stream in from the flanks. All the other enemies in the map will converge on the squad. And there game’s third most dangerous enemy type–the Scylla–is also there.
Thankfully, there is a “restart” button to click whenever brutal RNG hands the player an unfair hand with either mission layout of the variety of enemies on the map.
Haven’t played Battletech too much, but I think that there progression is more predictable than in Phoenix Point. It was easier to balance that game over the PP skill and leveling system. Here you have huge RNG factor about what tech you will get, depending on what faction and what events you will get at the start. PP is really hard to predict what player will get. Of course there could be some algorithm adjusting each mission depending on what player will really send to the mission… But wouldn’t it be strange that if we will send Manticore 1 with hero squad and we will get all advanced Pandorans, and if we will send Manticore 2 with rookies then we get basic Pandorans? That would be really artificial.
Probably solution to that would be decreasing power obtained by the player. Level-7 soldiers would need to be far less powerful than they are now. And replace it by equipment power which would be similar no matter which soldier player is using. Then ensuring that some equipment isn’t accessible too early… and ensuring that same equipment will be obtained at some specific point in time… That would make Phoenix Point a different game. 
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Fully agreed with the OP.
The game is broken. Always has been.
The game is unplayable.
The game serves as a perfect example of how to take an excellent idea/concept and trash it.
I am an early supporter. Tried to warn them 3 years ago. They were to arrogant to listen.