I would say that yes, it does make a difference in my experience. Several factors come into play. First, I always found that partial wort boils wound up with a darker end-product for me (although I was boiling significantly less than 4 gallons, probably more like 2.5). Second, I think it also created a bit more 'twang' factor that made me think the 'extract' flavor that many describe as 'extract twang' was more a byproduct of partial wort boiling since it went away with full wort boils, even those using extract. Third, yes, you'll need to plan your recipe around that dilution.