latex and word template for conference submission
Both LaTeX and Word support similar font packages (e.g., Times New Roman). So you could simply ask all authors to use the same font family (or set up the templates to do so).

What happens afterward depends on who's the publisher. If it's published in-house, both versions may just be published "as is." However, if an external publisher is used, both versions will likely be transferred to the publisher's "house style."