You're using a package which is very opinionated about how things with Git should work, so don't be surprised if related Emacs configuration which works without Magit gets clobbered when you do use Magit.
In this instance, Magit uses git-commit.el which provides the variable git-commit-major-mode for controlling this.
If you want to control how things happen ...
No, it is not possible. diff-mode is just for showing and editing diffs; VersionControl what gets committed, and works only with files or sets of files:
[some] version control systems [...] are file-based: each file has its own [...] history [...]. [...] changeset-based [systems' commits] may include changes to several files, and the entire set of changes ...
Choose your tool
If you have installed ag and not rg then ag will be used according to the documentation string in your dotfile you can see that Spacemacs tries the search tool in this order first rg, then ag, pt, ack and finally grep.
Hack your tool
One solution is to use the options of the tool you are using in your case for ag:
create a .agignore ignore ...
These versions are also called "stages" and the command to pick on is magit-checkout-stage. You can invoke that using M-x of course, but you can also just press k (magit-discard) on the conflicting file to discard the other stages. (But be aware that this prompts you for which side to keep, not which side to discard.)