In Surah 41:11, "come ye together" is, according to the Arabic, like if we were to call to people at the same time (i.e. we would call them together). This is not a melding together. It is not understood that way at all.
Nevertheless, I understand why you may jump to that conclusion. I read A. Y. Ali's comment and he understands the verse to be mentioning that the heavens and earth, once created, were meant to be kept together, not separate. However, he doesn't say he understands them to be joined together as one unit as Surah 21:30 says. I really do not know what A. Y. Ali means. Perhaps arranged together? In any case, regardless what A. Y. Ali's interpretation is, the Arabic is clear.
Let me stress the point, the Arabic word in Surah 41:11 means "come both of you", and then God asks them to submit. In Surah 21:30, the arabic means "one piece". To summarize, it is only the translation which could even give someone the idea that there is a contradiction. This is a reason why a Muslim does not regard translations of the Qur'an as the Arabic Qur'an itself.