Having worked at ZRH for more than 15 years in the passenger services, in my opinion, you should now ask the airline to refund your train ticket, not SBB. It is now too late for a compensation with SBB because the SBB Travel Centre at Zurich Airport has to hand-in the physical vouchers to the airline for their compensation.
Please kindly note, it was not SBB’s fault that the flight had been diverted. Consequently, they were not prepared for it. That a special counter is assigned to handle the irregularity, say to deal with customers having a voucher, is regular business. They do not want customers to block all the counters, as there are other travellers who do not want to miss their connection due to your irregularity. In case of an irregularity, delays are common and to be expected. Every customer on your flight was in the same situation, and possibly also arrived 3 hours later or even later at their homes.
You were impatient and decided to go on your own. Fairly doable, but you cannot claim a refund later through other channels as you were not adhering to the procedure as instructed by the airline. Therefore, my advice, contact the airline and hand-in your SBB ticket for compensation while explaining the situation.