Currently, in an automated setup with Industrial Foregoing and Chickens / Hatchery / More Chickens I can not use the main source of fertilizing material (Chicken Manure). Could this be added?

There's currently no APIs on Industrial Foregoing for the Plant Fertilizer, but I can get that sorted.

Awesome. Will that come as a new release, or something I should change on my end?

There will be a new version of Industrial Foregoing adding the API first, once that update is released, I will be able to add the integration on my side using the API and then a new version of Integration Foregoing will be released. You don't have to change anything on your end, just make sure to keep both mods up-to-date. I will be closing this issue once the integration is added, so don't worry. :)

Apparently this has been added via allowing the fertilizer OreDict to be used, so I don't have to do anything on my side I guess.
InnovativeOnlineIndustries/Industrial-Foregoing@a152b73

Sadly this still does not work (chicken manure doesn't count as a fertilizer I guess). Should I maybe take this to Industrial Foregoing instead of Integration?

You should do if it doesn't work, since my addon can only help with integrations that are able to be added via the API.