Why is a PacBio read length larger than the aligned reference region?
Q1
Probably not - this is probably just displaying the contents of the input (I presume a bam file) exactly as they are encoded.
Q2
The splicing looks a little weird, but the exon-mapping pattern in the 5' part of the gene makes it seem like RNA rather than DNA. I think that the large intron is what makes you think that it is DNA, correct?

Explanations for weird splicing

The weird read is a rare splice variant but a true mRNA.
The weird read is not completely matured and has an intron that has not yet been spliced. The IsoSeq library prep protocol picked this up somehow and it ended up being sequenced.



Q3

Explanations for why Seq length: 6751 and Seq length on ref: 5267

There is probably a large amount of clipping on the 5' or 3' end of the read. This could be polyA or some other transcribed-but-not-yet-completely-matured seq. Or, the extra sequence could be sequencing error, PacBio adapters, or a chimeric molecule.



things to try
How to check what is going on:
I'm guessing that you had to upload a bam file to JBrowse to make the IsoSeq track. Use the sequence name that you got from Jbrowse and run the following command to extract the alignment info from the bam file:
samtools view /path/to/your/isoseq/file.bam | grep 'weird_read_id'

Look at the cigar string to see what it says about 5' or 3' clipping and corroborate with the sequence data.