After several discussions on both sides, what you said is also what we have found. I have a feeling the negative attitudes toward side-venting came from problems in the 90s with first-gen high-efficiency furnaces. Now the questions is simply of cost, and the decision has been quite difficult for us - chose between a necessary repair and an unnecessary upgrade to avoid that repair and any problems later on...
Option 1: $4300-5300
Rebuild, reflash, reline: $4300
Possible roofing repair: ~$1000
Option 2: $6100
Replace furnace: $3700 - rebates/credits = $3200
Replace water heater: $1700
Remove chimney, patch roof: $1200