TDM mostly modifies the AI files. The only change in the Data folder is the addition of a number of extra formations. If your personal mod works with stock game AIs, combining them as you asked would definitely work.
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And a quick question about modding AI designs.
I have made a large (x3) and massive (x5) Shipyard component for orbital starbases, but when the computer designs those sized construction bases it fills them with nothing but shield generators, it doesn't even use the 'normal' sized shipyard component. How (and what) do I need to change to fix that?
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How large are your new space yards? The AI designs vehicles by traversing the design in the corresponding AI_DesignCreation.txt file in its ships folder. It might not have enough space to add the large space yard component when it gets to it in the list.