Misalignment in Earth observation (EO) images and building labels impact the training of accurate convolutional neural networks (CNNs) for semantic segmentation of building footprints. Recently, three Teacher-Student knowledge transfer methods have been introduced to address this issue: supervised domain adaptation (SDA), knowledge distillation (KD), and deep mutual learning (DML). However, these methods are merely studied for different urban buildings (low-rise, mid-rise, high-rise, and skyscrapers), where misalignment increases with building height and spatial resolution. In this study, we present a workflow for the systematic comparative study of the three methods. The workflow first identifies the best (with the highest evaluation scores) hyperparameters, lightweight CNNs for the Student (among 43 CNNs from Computer Vision), and encoder-decoder networks (EDNs) for both Teachers and Students. Secondly, three building footprint datasets are developed to train and evaluate the identified Teachers and Students in the three transfer methods. The results show that U-Net with VGG19 (U-VGG19) is the best Teacher, and U-EfficientNetv2B3 and U-EfficientNet-lite0 are among the best Students. With these Teacher-Student pairs, SDA could yield upto 0.943, 0.868, 0.912, and 0.697 F1 scores in the low-rise, mid-rise, high-rise, and skyscrapers respectively. KD and DML provide model compression of upto 82%, despite marginal loss in performance. This new comparison concludes that SDA is the most effective method to address the misalignment problem, while KD and DML can efficiently compress network size without significant loss in performance. The 158 experiments and datasets developed in this study will be valuable to minimise the misaligned labels.