Is there any reason to ever side with the UTA?

Solution 1:

From the Space Pirates and Zombies wiki:

The main benefit of having good relations with the UTA, aside from being able to wander near their ships and stations without being attacked, is that Friendly bases can be bribed with goons to let the Clockwork pass through one or more warpgates. This is the only other way to open a warpgate besides fighting its UTA blockade.

The story does change these mechanics:

Also, Chapter 4 drastically alters the Faction mechanics, including those of the UTA. The UTA join forces with the Clockwork against the zombies and will always be at Ally status in every system. The player can upgrade the UTA's starbases for a Rez and Goon cost.

Each local UTA faction works to protect their system from invasion. Each system will have a "defender strength" that will fight against the corresponding strength of any zombie invasion. The higher the strength of the UTA starbase, the higher the cap on system defender strength.

Solution 2:

UTA bases sometimes have parts for sale that require at least neutral, like, or friendly status. Whether or not they have items for sale is visible on the Galaxy map by a circular green "$" symbol next to the star system as well as next to the base in question within the solar system.

In addition to that, you gain the ability to do commodity trades between goons, rez, and data or bribing to pass a warp gate.

This is all true for both UTA and civ outposts in the various solar systems. An outpost will not let you buy the ship part with a bad reputation and as such it is advised to work towards buying the UTA part first (increasing UTA rep) since your civ reputation will usually go down as a result. Then after getting what you need from UTA, you can get your civ rep up if they are selling items which often results in UTA rep going down. You can then move on to killing UTA warp gate blockades without worrying about rep.

Solution 3:

In the early part of the game, having neutral or better relations with the UTA permits you to:

• Buy parts/upgrades from them via black market
• Trade with the station for its resource (ie, Goons, Rez, Research points)
• Bribe the UTA to allow access to the next system via a gate.

It can be very effective to bribe a strong UTA presence to allow you access to the next sector rather than fight the guard force. Being able to trade with a UTA station for its resources can help you set up quickly upgrade your ship/fleet.

While it is possible to destroy a starbase to gain access to the parts/upgrades it sells, this will reduce the strength of that starbase by 1 level when it is rebuilt. There are reasons to leave the starbases, both civilian and UTA, as strong as possible, due to later game events when those strength levels will be more useful to you in game.