The scans were done on teens who identified as trans and who had transitioned (do not know whether just socially or also medically). Because as PP have pointed out our brains are plastic and elastic, it is only to be expected that the brains of children who typically identify with stereotypes of the opposite sex very strongly, should exhibit functional connectivity (FC) patterns typically observed in opposite sex children. It's a bit of a chicken/egg scenario - do their brains light up in that way because they are identifying as trans or are they identifying as trans because their brains light up in that way?
Fact is that earlier studies looking at functional connectivity in pre-pubescent children of both sexes and all genders found zero differences. And as we know, the brain is massively restructured during puberty. Because the researchers did not include other children in the study, we can't for instance even compare these findings with those of GNC but non-dysphoric children or those sharing the same sexuality. It's entirely possible that brain scans in GNC children would find similar patterns.
In any case, such claimed male/female functionality patterns are now understood to be a consequence of rather than a cause for sex stereotyping in our society. The researchers here are certainly at odds with other recent findings that showed that if you gave a million MRI scans of 50/50 men and women to researchers to sort into scans of males or females, it would be an impossible task.
So, the premise of this study is already highly questionable given that it claims to a) have identified typical male or female patterns in the brain (with the accompanying stereotyping at its finest) and b) be able to differentiate those patterns strongly enough to be able to quantify what classifies the brain scan of a male child who identifies as trans as sufficiently female-patterned to posit this is proof of their being trans.
Given no male or female FC patterns were found in younger children this study may provide a jumping off point for further research but delivers nothing of any substance.