The MX-5000 and the Harmony should probably not be used in the same post when looking for suggestions. Even if the URC appears to be more primitive than the URC remote the Harmony will simply not program better. All the "behind the scenes assumptions" a Harmony remote tends can make for some hair pulling experiences. Most if not all of the customer I have sold controllers to, did some work for, or utilize other services have had a harmony in the past. They have since graduated to better controllers that complement their system and they can be made to be more customized for the experience.

URC Professional Series remotes will all work in tandem with each other as long as you are using an MRF-260 & MRF-350 extenders and MSC-400 control processor. The budget you have indicated is not going to work with an MX-5000 which has two way control, haptic feedback, full graphic customability, wi-fi, and other features that are premium to the lower tier remotes like the MX-350, MX-850, MX-780, & MX-900. However, the lower tier remotes are extremely reliable and program well. All of these remotes and the higher models have IR port routing

Please note that URC remotes are not wizard based and the professional series are best purchased through an authorized dealer who can program them as well.