I like and have considered having various mutually exclusive or independent paths through game content.
I'm glad you discussed the in-game meaning of different content pathes, as the issue of how to make the various options different from a gameplay perspective is more important than picking things like what to call the options, (eg. "mechanical" vs. "biological" tech). We can likely find plausible sci-fi story justifications for any interesting divergence in gameplay nature of content.
Using gameplay mechanics to differentiate can be done partly by taking advantage of content other than techs, or paths through the tech tree to unlock a certain set of same-effect but different-name abilities, though.
One path through the content could be focused more on having lots of production capacity, with buildings that boost production themselves requiring lots of production for an empire to create, while a separate path would be more research focused, with lots of research-boosting techs themselves costing lots of research points.
A separate set of pathes would be between various ship tech branches
where there are clear and prominent distinctions between the branches in terms of what pros and cons the various hulls have.
The biological approach could have a advantages with food production, population and health. Later it could become better suited for environments with water and moderate temperatures, like swamp or ocean worlds.
Preference for one set of planet environments over another is probably something that races should deal with, unless it can be done in a way that will make the difference equally useful for any racial environment. It's not necessarily bad to have one race be more or less suited for a particular tech path, but indirect dependence through which environments can be modified is a potentially strange and unclear way to set that up.
Terraforming vs. self-modification is a nice pair of options, possibly which could be a triad with exploration / expansionism. These could be useful for having "moral" choices that certain populations could prefer or dislike, to make chosing have more consequences for population preferences.