The 3' and 5' flank refer to the transcript(s). Using Dynamic filter for Function, VarSome Clinical will mark a variant as flanking if it is within 500nt of a transcript's start or end position. UTRs are part of the transcript, and such shouldn't be an issue.
If you have a particular set of regions, we could filter the result for those regions. Alternatively, you could run a gene list analysis, limiting the results to only the list of genes.
Another possibility, if this is something you will often be doing, is setting up what we call Algorithmic filters. These are more sophisticated filters that run as separate analyses and there we can write one catering to whatever specific filtering you require. In that case, we could search for coding variants in all genes and also include any found in the upstream regions of the target genes.