The general rule with FreeREG is to include everything which could possibly be of genealogical interest, which usually means everything except the minister's name (and even that should be included sometimes, e.g. if a wedding was conducted by a minister from a far-off parish he may well be a relative of one of the couple). Some files are copied from older paper transcripts rather than the original register or converted from digital transcripts not originally intended for FreeREG, and these may not have all the details, for example leaving out the witnesses to marriages. They will be revised as and when better source material becomes available. In many cases the church name in a FreeREG record is followed by PR, BT or TR to indicate whether the source was the parish register (or images thereof), the Bishop's Transcripts or a previous transcription respectively. Many older files don't have this indication.
You can find details of the coverage of each Somerset parish here:
http://www.freereg.org.uk/parishes/som/frontpage.shtmlBlagdon currently has baptisms 1800-1819 from the parish registers but nothing from the 1700s. Nempnett has up to 1807 from the registers and 1813-1836 from the BTs. So each has gaps around the time John Clark would have been born. However, there was a John Clark baptised at Nempnett in 1797 or 1798. (The date is illegible but it comes between entries from Nov 1797 and Apr 1798.) His parents were James and Seacey or Leacy. (They have 5 children baptised there, from Ann in 1788 to Benjamin in 1801, the transcriber has read the mother's name differently nearly each time - Se_cey, Loocy, Loucy, Leacy.)
I notice Benjamin married at Nempnett in Oct 1826 - a few months after John married Fanny - and one of the witnesses was Frances Clark. So it looks quite plausible that it is your John in 1798, a little older than suggested. But on the other hand if parental consent was required for the wedding in 1826, at least one of the couple should have been under 21 at the time, and so born after 1804.
(But nearly every wedding at Blagdon 1822-1827 is shown as "with parental consent", so there may well be a misunderstanding there.)
DAvid