The study of inter-annotator agreement in musical pattern annotations has gained increased attention over the past few years. While expert annotations are often taken as the reference for evaluating pattern discovery algorithms, relying on just one reference is not usually sufficient to capture the complex musical relations between patterns. In this paper, we address the potential of digital annotation tools to enable large-scale annotations of musical patterns, by comparing datasets gathered with two recently developed digital tools. We investigate the influence of the tools and different annotator backgrounds on the annotation process by performing inter-annotator agreement analysis and feature-based analysis on the annotated patterns. We discuss implications for further adaptation of annotation tools, and the potential for deriving reference data from such rich annotation datasets for the evaluation of automatic pattern discovery algorithms in the future.