Yes, you can use Linchpin features within other theming plugins. The problem is, that we do not test against such apps and you may run into problems. We will support this and try our best to help you. It's most likely a degraded and a little cumbersome experience.
I understand that it may seem hard to change something that does not fail.
But following our solution including the adoption of our theme ensures the best usability and a seamless experience both for your project team during the configuration phase and for your users later. Not using this combination will make you loose a lot of onboarding traction and wow effect in exchange for some same-same and some "looks as always".
There are also a lot of features that are directly intertwined with the layout. When you choose a layout in our Linchpin Theme Plugin it will automatically travel into the news layout, the navigations, the app center and other parts of Confluence without additional work. The Linchpin mobile app will soon be able to have your company colors and your logo, but only if you use the Linchpin Theme Plugin.
Another big downside is the maintenance of a self-made solution. Atlassian is an innovative company that often releases new versions and new features. The more apps you install, the more difficult your upgrade path is. With Linchpin we take care of this whole experience for you. All of our apps are "verified by Atlassian" and we work closely with other vendors to make sure, that upgrading is a matter of minutes for you and not an individual hassle with a lot of back and forth between vendors.
To cut a long story short: Linchpin Theme Plugin costs a fraction of Brikit, saves you money and seamlessly integrates in the overall experience of Linchpin Intranets. We highly recommend that you use it.
Check out our comparison between Brikit Theme Press, Refined Wiki and Linchpin Theme Plugin
Intranet Theming Comparison