It could be detected by the softare, and depending on the requirements of the journal and/or the conference you could have the paper rejected by one or both venues.
In most disciplines, journals only accept submissions that are new and not previously published elsewhere in any form with the possible exception of papers based on MS/Ph.D. theses. Journals that take this stance would typically consider "published on a website" as published. The conference organizers are warning you that appearing on this website could be considered publication.
In some disciplines, it is more common for journals to allow for extended versions of shorter conference papers to be published later as journal papers. However, there must be some significant expansion and rewriting of the paper and it is important to disclose the prior publication when you submit such a paper.
If the journal has a "must be original, not previously published" rule and they discover that you've broken that rule, your paper will be rejected and you may be blackballed from any future submission to that journal.
So, check the submission guidelines for both the journal and the conference before submitting your paper. If the conference doesn't mind and the journal is willing to accept an extended conference paper then you should disclose that you've submitted a shorter version of the paper to the conference when you submit your extended version to the journal.