Summary and Info:
When using makepkg's --rmdeps option, if an old dependency required by package A is replaced by a valid make dependency of package B, makepkg will tell pacman to remove the make dependency of package B and fail because it is a required dependency of package A, resulting in no make dependencies being removed at all.

[blackarch@bender test]$ makepkg -sirp another-pkg.pkg |& tee makepkg.log
==> Making package: another-pkg 1.0-1 (Wed Jan 8 01:40:38 UTC 2014)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Installing missing dependencies...
resolving dependencies...
looking for inter-conflicts...
:: new-foo and old-foo are in conflict. Remove old-foo? [y/N] y

Packages (3): old-foo-1.0-1 [removal] another-foo-1.0-1 new-foo-1.0-1

Total Download Size: 0.00 MiB
Total Installed Size: 0.00 MiB
Net Upgrade Size: 0.00 MiB

:: Proceed with installation? [Y/n]
:: Retrieving packages ...
downloading another-foo-1.0-1-any.pkg.tar.xz...
checking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
removing old-foo...
installing new-foo...
installing another-foo...
==> Retrieving sources...
==> Extracting sources...
==> Removing existing pkg/ directory...
==> Entering fakeroot environment...
==> Starting package()...
==> Tidying install...
-> Purging unwanted files...
-> Removing libtool files...
-> Removing static library files...
-> Compressing man and info pages...
-> Stripping unneeded symbols from binaries and libraries...
==> Creating package "another-pkg"...
-> Generating .PKGINFO file...
-> Generating .MTREE file...
-> Compressing package...
==> Leaving fakeroot environment.
==> Finished making: another-pkg 1.0-1 (Wed Jan 8 01:40:41 UTC 2014)
==> Installing package another-pkg with pacman -U...
loading packages...
resolving dependencies...
looking for inter-conflicts...

Packages (1): another-pkg-1.0-1

Total Installed Size: 0.00 MiB

:: Proceed with installation? [Y/n]
checking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
installing another-pkg...
==> Removing installed dependencies...
checking dependencies...
error: failed to prepare transaction (could not satisfy dependencies)
:: some-pkg: requires foo
==> WARNING: Failed to remove installed dependencies.

[blackarch@bender test]$ pacman -Q another-foo
another-foo 1.0-1


Steps to Reproduce:
1. Build the attached packages: old-foo, new-foo, another-foo and some-pkg
2. Install old-foo
3. Add new-foo and another-foo to a repo and add that in pacman.conf
4. Run pacman -Syyu
5. Install some-pkg
6. Attempt to build and install another-pkg via `makepkg -sirp another-pkg.pkg`

This results in any make dependencies of another-pkg (e.g. another-foo) not being removed as expected. And while new-foo should not be removed, another-foo should.

A real world test of this can be seen when the base-devel group is installed but not the multilib-devel group and a package like lib32-smpeg (https://aur.archlinux.org/packages/lib32-smpeg/) is installed. The make dependency lib32-glu is still installed and required by nothing, but it not removed because gcc-libs (provided by gcc-libs-multilib) is required by a number of other packages. A log is attached for that scenario.