X-ray micro-computed tomography (micro-CT) has been widely leveraged to characterise pore-scale geometry in subsurface porous rock. Recent developments in super resolution (SR) methods using deep learning allow the digital enhancement of low resolution (LR) images over large spatial scales, creating SR images comparable to the high resolution (HR) ground truth. This circumvents traditional resolution and field-of-view trade-offs. An outstanding issue is the use of paired (registered) LR and HR data, which is often required in the training step of such methods but is difficult to obtain. In this work, we rigorously compare two different state-of-the-art SR deep learning techniques, using both paired and unpaired data, with like-for-like ground truth data. The first approach requires paired images to train a convolutional neural network (CNN) while the second approach uses unpaired images to train a generative adversarial network (GAN). The two approaches are compared using a micro-CT carbonate rock sample with complicated micro-porous textures. We implemented various image based and numerical verifications and experimental validation to quantitatively evaluate the physical accuracy and sensitivities of the two methods. Our quantitative results show that unpaired GAN approach can reconstruct super-resolution images as precise as paired CNN method, with comparable training times and dataset requirement. This unlocks new applications for micro-CT image enhancement using unpaired deep learning methods; image registration is no longer needed during the data processing stage. Decoupled images from data storage platforms can be exploited more efficiently to train networks for SR digital rock applications. This opens up a new pathway for various applications of multi-scale flow simulation in heterogeneous porous media.