Yes, it is limiting and no it isn't.
The limit is primarily on a cognitive level: the design guidelines - and more importantly: the apps adhering to those, including built-in apps - will be the base of your users' expectations.
In order for an interface to be intuitive, it has to work in familiar ways.
Even on the web, we do have expectations: I expect input boxes to have a white background for example. Or that only errors or other important notifications should be red.
For example, Nielsen wrote this about search box expectations:
Users now have precise expectations for the behavior of search.
Designs that invoke this mental model but work differently are
On the same note, it's one of the top 10 big mistakes to devoid conventions unnecessarily.
You can do so in small / closed user bases but you won't have world-wide success with a special UI. Perhaps it fits in an industrial context however - but if you are for a consumer market, I'd vote for against anything too unconventional.
Take the case of Prezi *: Originally they had a very custom UI. I remember the founders deeming "such an unconventional approach needs an unconventional UI". But it wasn't until they have changed the UI in 2012 into a much more conventional, much more-powerpoint like user interface that had a huge positive impact in usability for them.
This is how it evolved, have a look at it for yourself.
(Disclaimer) * I was a workmate of the founders and know each and every user researcher of Prezi personally.