Matthew, Thomas' profile as it originally existed was based on speculation. There were no BMD records, wills, or land records to support the connection of his parents (John and Agnes) or several previously attached children. The profiles that were detached were detailed in the research notes. If evidence is found that any of the disconnected children were actually Thomas and Joan's, they can easily be reconnected.
Pre-1500 profiles on WikiTree are very often connected to the wrong ancestors. IMO, it's much better to disconnect false lineages than to perpetuate incorrect genealogy.
Thank you to Nic, Helen and Vance for your research and finding evidence that Thomas was the son of William. I've added new profiles for William and his wife Isabella. Apologies for my delay in responding ... I've been offline for the last 10+ days.
Please feel free to edit these profiles as needed. I will look into them further eventually.