There are several reasons why merging mods can be a pain...
Manifests -- Sins uses several manifests to "tell" it what files to load at game start up...take for example the entity manifest, which tells the game all the entity files that need to be loaded...consider a very simple mod which changes one targetted ability to an AoE...it is very likely you will need to add a Buff file to make this happen, and consequently your mod will need a new entity manifest that includes the name of this new buff file...
Most mods make changes to the entity manifest, and thus when combining any two mods, you need to make a new entity manifest that lists all the files used by both mods...in theory, a computer program could do this...it could read the two entity manifests, and create a 3rd manifest that doesn't have multiple references to the same file...
Universal files -- Most mods make changes to the GalaxyScenarioDef and the Gameplay files...to combine any two mods, you would need to go through each of the modded versions of these files and synthesize the changes to a 3rd instance of the file...in theory, a program could do this barring no conflicting changes...but, most mods are likely to have conflicting changes or different naming schemes...
To give an example, say mod A doubles the tax rate on planets but mod B halves the tax rate...which value do you pick? When combining two mods with conflicting changes in the Gameplay file, often a judgment call is needed and thus these files have to be done by hand, not by a program...
To give another example, suppose mod A uses a different naming scheme for planets than mod B...a computer program would simply copy each mods references to planets in the GalaxyScenarioDef because they technically have different names...in reality though they are the same entries, just with different naming schemes, and a person is going to have to go make the necessary changes by hand...
Balance -- More involved mods that change lots of things related to gameplay can't be easily combined simply because the balance would be totally wonky...suppose Mod A (in addition to its other changes) makes Star Bases more powerful in the late game by increasing the number of upgrades a Star Base can have....suppose Mod B (in addition to its other changes) also makes Star Bases more powerful, but does so by allowing each faction to build 2 in every gravity well...
Both Mods (in addition to their other changes) wanted to make SBs more powerful but not too powerful...by combining the changes, you now have a mod with uber powerful Star Bases and therefore distorted balance...it's not hard to conceive of far worse balance situations...
In short, combining mods ultimately is going to require a lot of judgment calls and changes that can't be done by a program...occasionally a basic program might come into great use, but it will likely be very specific to the two mods you are trying to combine and thus of little use to other people....it is true that a program can often be re-purposed to do a similar task, but usually the source code would be needed to make those changes and most modders are not familiar with all the various languages one might use (C++ and java are probably the two most common)...
