Could it have something to do with the custom-homepage plugin overriding the home.tpl template?
Perhaps, but I'm not totally sure.
The way I place widgets is I just take whatever is a widget template and copy and paste it into one of the main theme templates such as topic.tpl or category.tpl.
So for example, the popular tags widget (which I have not used yet but will soon), looks like this.
<!-- BEGIN tags -->
<a href="{relative_path}/tags/{tags.value}" class="pull-left">
<h4>
<span class="label label-info">{tags.value}</span>
<small>x</small><span class="tag-topic-count">{tags.score}</span>
</h4>
</a>
<!-- END tags -->
I take that and place it somewhere (anywhere) I want it to render in a template.
-_-
Another example is using the widget-area as shown here using the "active users" widget (this is for category.tpl);
Screen Shot 2014-07-23 at 3.51.41 AM.png
And the HTML is as simple as this;
<div class="category-active-users">
<div widget-area="sidebar"></div>
</div>
Whatever is placed in widget area named "Sidebar" in the ACP, is what will render here. For this I have simply used the "Active Users" widget block as shown below.
Screen Shot 2014-07-23 at 3.54.20 AM.png
All in all, its a matter of preference of how you want to do things.
