Yes. All kits have bias. All Illumina versions of anything (platform, software, etc) have bias too. So your data absolutely has bias, which is one reason it's best to only compare data using identical methodologies. If, for example, you wanted to do some kind of quantification with group A using kit W and sequencer X, and group B using kit Y and sequencer Z, your results would be complete garbage.
If all you care about is genome assembly, and not quantification, then it typically does not matter at all as long as you have sufficient coverage.