While that certainly creates cumulative disadvantages and advantages respectively, the amounts issue is quite peculiar because the applicants are the ones asking for a given amount. The most credible hypothesis is that people at the big universities believe they are excellent, so they tend to ask for more money for their research projects. That's a rather negative effect of the system: People in smaller universities ask for less money on average, so they're given less money as a result.
Again, there would be standardization measures that would be fairly easy to put in place to prevent that.