Yes, there is a difference. If you intend to run four modules, you're rolling the dice that there won't be any kind of issues. Even identical part number kits that came off the same production line can have issues with compatibility. If you want to run four modules it's highly recommended that you buy them all in one kit so you'll know they've already been fully tested for compatibility with each other.
Obviously, this isn't ALWAYS a problem, and quite often unmatched sets will run ok together, but there are plenty of instances where two sets of the same part number, or two entirely different sets that both have identical specs, will not run in dual or quad channel operation and in some cases won't play nice together at all. Not sure that taking that chance is worth the risk that they don't agree, just to save a few dollars.
If you happen to get two sets that don't work well together, and this can present itself in a variety of different ways such as just not being recognized, lack of proper channel operation, won't run at advertised speeds or won't run at advertised speeds without significant voltage increase, or just a lot of random glitches that you can't quite identify the source, that few dollars you saved might turn into shipping costs to return sets or RMA modules, and the expense of a terrible headache trying to figure out why.