You can (generally) manage the installation of packages together with their configuration.
You can override individual configuration values for different machines (which I guess, you can also do via templating in chezmoi).
Some programs don't have a particularly readable configuration file or spread this configuration out over multiple files, or save all kinds of additional garbage into their configuration file which you don't want to persist. Home-Manager can work around all these issues, and in such a case is likely also better documented than the original configuration file.

That last point is one that's particularly relevant for me, because KDE Plasma's configuration files are largely terrible. Home-Manager, together with Plasma-Manager, is the only sane way I know of, to automate the panel configuration in KDE.

But yeah, if you don't use software with terrible configuration files, then I can certainly understand preferring dumb templating. I have also decided against using the Home-Manager-specific modules in places, or might only translate into the Home-Manager-specific module when I actually want to vary configuration values between two machines.

Just to give a quick impression of how terrible the KDE panel configuration is, this is a snippet out of the fittingly-called plasma-org.kde.plasma.desktop-appletsrc file:

[ActionPlugins][0]
MiddleButton;NoModifier=org.kde.paste
RightButton;NoModifier=org.kde.contextmenu

[ActionPlugins][1]
RightButton;NoModifier=org.kde.contextmenu

[Containments][1122]
activityId=f588743a-9bab-4f56-8f90-3616085ab6e0
formfactor=0
immutability=1
lastScreen=1
location=0
plugin=org.kde.plasma.folder
wallpaperplugin=org.kde.color

[Containments][1122][Wallpaper][org.kde.color][General]
Color=#79740e

Ah sorry, that doesn't actually show any of the panel configuration, because KDE mixes configuration for the panel and desktop widgets and the Activities feature (like workspaces, but with separate wallpapers and widgets for each Activity) all into the same file.
So, here's a snippet that actually shows the panel configuration, from just a few lines below the first snippet:

[Containments][1807]
activityId=
formfactor=3
immutability=1
lastScreen[$i]=0
location=5
plugin=org.kde.panel
wallpaperplugin=org.kde.image

[Containments][1807][Applets][1808]
immutability=1
plugin=org.kde.plasma.showActivityManager

[Containments][1807][Applets][1810]
immutability=1
plugin=org.kde.plasma.pager

[Containments][1807][Applets][1810][Configuration][General]
showOnlyCurrentScreen=true
showWindowIcons=true
wrapPage=true

[Containments][1807][Applets][1811]
immutability=1
plugin=org.kde.plasma.panelspacer

[Containments][1807][Applets][1812]
activityId=
formfactor=0
immutability=1
lastScreen=-1
location=0
plugin=org.kde.plasma.systemtray
popupHeight=432
popupWidth=432
wallpaperplugin=org.kde.image

What those numbers in e.g. [Containments][1807][Applets][1812] are? Ah, they just count those from 0 to infinity, whenever you add a widget through the UI.
And in case you were wondering since when INI allows for nesting section keys via [multiple][brackets]: It doesn't. That's a custom extension of the INI format, specifically in use by KDE.

Like, man, I love KDE for its features, but this is the stuff of nightmares.