I have seen civilian engineers further a development program or support another engineer's investigation without benefit to their own advancement opportunities. Some put in extra hours and work weekends without extra compensation or, special recognition. It can be frustrating to expect needed corporate loyalty and organizational pride front these latter individuals, especially when they identify more strongly with neighborhood or community organizations than with their workforce. My perception of pay scales and performance rewards is that opportunities are essentially equal for military and civilian personnel. The higher basic salaries of the civilian employees are sometimes offset by incentive pay for rated or engineering duty that the military receive.
Military engineers have better access to government-sponsored graduate education.
Both military and civilians are promoted based on performance ratings, and both compete for organizational awards that recognize technical or managerial excellence. My personal view is that most professionals react more favorably to opportunities to wield greater authority or solve problems of greater significance than to strictly monetary rewards. There are other, often overlooked, differences between military and civilian research and development employees that are no less significant for their subtlety. Until recently, military engineers have had a specified wartime duty position, typically in a zone of hostilities, to which they would mobilize if required for national defense. All rated military engineers still retain a flying position as their primary duty identifier and fully expect to be mobilized to flying duties in times of national emergency.