Being in /etc made it a conffile by default which is what will give it all the 
handling about updated files that you were facing.
I agree that in general this would be a file one expected to be around in an 
informal way, but not be bothered with these questions.

IMHO this should be moved to e.g. /usr/share/postfix/makedefs.out
And yes there could be a symlink from the former /etc path, but I think that 
isn't strictly required.

Just like this maybe:
diff --git a/debian/changelog b/debian/changelog
index cfbe1683..fd2c3b45 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+postfix (3.2.4-2) unstable; urgency=medium
+
+  * make makedefs.out no more be a conffile Closes: #908545
+
+ -- Christian Ehrhardt <[email protected]>  Thu, 13 Sep 2018 
14:23:22 +0200
+
 postfix (3.2.4-1) unstable; urgency=medium
 
   [Wietse Venema]
diff --git a/debian/postfix.maintscript b/debian/postfix.maintscript
new file mode 100644
index 00000000..7a81ec99
--- /dev/null
+++ b/debian/postfix.maintscript
@@ -0,0 +1,2 @@
+# moved to sharedir to not bother users with conffile prompts
+rm_conffile /etc/postfix/makedefs.out 3.2.4-2~ postfix
diff --git a/debian/rules b/debian/rules
index 59ca3d7d..a6a3bb20 100755
--- a/debian/rules
+++ b/debian/rules
@@ -174,7 +174,7 @@ install-arch: build-arch
        ln -s ../sbin/sendmail $(bindir)/mailq
        ln -s ../sbin/sendmail ${base}/usr/lib/sendmail
        install -m 0755 conf/postfix-script conf/post-install $(confdir)
-       install -m 0644 conf/makedefs.out $(confdir)
+       install -m 0644 conf/makedefs.out $(sharedir)
        install -m 0644 debian/functions $(sharedir)/postinst.functions
        install -m 0644 conf/master.cf $(sharedir)/master.cf.dist
        install -m 0644 conf/main.cf.dist $(sharedir)/main.cf.dist


I'll suggest that to the Debian bug.

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https://bugs.launchpad.net/bugs/1791853

Title:
  Postfix upgrade queries about replacing /etc/postfix/makedefs.out,
  when it really should always do so

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