The judge may have erred by solely looking at the Federal Court Rules (rule 400 in particular) when determining Teksavvy's obligation to notify customers. They have an obligation to notify under PIPEDA which the judge did not account for. The bulk of the $350,000 Teksavvy was requesting was for council - the judge may have also erred here. In the first hearing the judge stated that costs would be addressed at a later date and punted the issue. When costs were finally addressed by the current judge they said "it's too late to address those particular costs". ie: the problem was procedural not whether or not Teksavvy deserved to have the costs reimbursed. There were also some costs which TSI has to prove before they can be paid for them.
Likely what is going to happen is that TSI will appeal the ruling and get another ~$150,000 or so of the $350,000 requested (somewhere around the $180,000-$220,000 range including the $22k already ordered). The 'tone and spirit" of the previous case you linked is one thing but there's also the costs awarded every time the police request an IP correlation for a criminal case. Those cost awards are in the $100-$150 per IP range... this was $11 per IP. Not exactly consistent with existing precedent.