"Before the war, Fallback scouted newly discovered worlds to determine if they were suitable for colonization. Now his duty is to assess a world's environmental health and recommend ways in which the Autobots can protect it while also using natural resources to their advantage."

To me, the key word is "now." Fallback used to find new worlds for the Autobots to colonise, but now (implying that he wasn't doing so before), he helps the Autobots can live in a mutually beneficial way on their host planet. It implies that previously their policy with living off-world was quite different. Although exactly how it differed is not explicitly stated, the use of the word "now" implies that it may have been very different to their current policy where they take the host planet's environmental welfare into consideration. It's not exactly a reconciliation with any sapient species per se, but rather an amendment of the way the Autobots now see living off-world where they no longer wish to simply plunder/exploit natural resources.

I see it as an allegorical reference the initial relationship between Whites and Indigenous Australians during colonisation and the current relationship which strives more toward one of mutual respect; but in Fallback's case, it's talking about mutual respect for nature where there previously wasn't. That's how I see it anyway.