There is an idiom in English: "comparing apples to oranges", which is used by people in discussions when they think a comparison is invalid, because the two things being compared are too different.
e.g. If I were to compare driving a car to piloting a boat, to see which is better, it would be like comparing apples to oranges.
What your quoted statement is doing is countering the argument that you can't compare apples to oranges.
It is saying that IBM Lotus Domino and Microsoft Sharepoint are (metaphorically) both fruits grown in an orchard, therefore they can be given the higher level comparison between fruits from orchards. This is because they may not be the exact same type of software, but their functionality is close enough that comparisons can be drawn.