If anything, you might be *extending* the life of your trans. Here's why...
Torque Management allows for nice pillow-soft shifts. Lots of people like a soft (even imperceptible) shift - but to get that, friction is introduced - and friction creates more wear. You'll feel the shifts more as a result, by disabling it, but there will be less slippage / friction. IIRC, Torque Mgmt adjusts the shift by manipulating the throttle response.
I'm actually having Lime-Swap flash my PCM as well - sent it off today (but I'll have to wait a week because Jeremy's going on vacation). I mention this because I had sent him a note a few months ago with some questions & to give him some background of what I was looking for - he was happy to provide recommendations on Torque Mgmt & other parameters as well.
The nice thing is, if you don't like the changes, it can always be flashed again (although there's a $25 charge for doing so - you probably saw that on his website.)
Turning 'off' PWM engagement can have an even greater benefit for trans longevity than adjusting Torque Mgmt. PWM is used to engage torque converter 'lockup', and also has a role in shift 'quality' - but it does this via a 'TCC' valve that tends to wear in its bore, and by continuously 'slipping' the torque converter. Slipping = friction = wear (sound familiar?)
Many people on this forum (myself included) have installed corrective shift kits in order to guard against / correct the TCC valve issue above. So you're doing much the same thing, only via software. Now, if it's actually being turned 'off'... I don't know what that will do for 'lockup' on the Torque Converter - when you get into lockup, you're running the engine about 300 or so RPM lower than it normally would in 4th gear - which helps with fuel economy. So if it's 'off' - will you lose TC lockup altogether? (I'm not sure)
The shift kits I mention above turn it into an 'on / off', where lockup winds up feeling like a 5th gear - and we can kick it right out of lockup as well (ex: engaging passing gear, or closing the throttle outright / braking.)
Our kits eliminate the 'pseudo-lockup' in the higher gears, which is what happens with the stock setup - the vehicle goes continuously into / out of lockup as road / load conditions dictate. That is eliminated with our shift kits, but we can still get into lockup at steady state cruise in 4th gear. Hopefully, you can do the same, via the flash.
Worst case if you lost lockup entirely is that you might lose 1 mpg or so if you're taking a longer highway trip. While I'm happy to have control over lockup, if it were a choice between "losing it altogether and taking a small MPG hit" and "having it but putting more wear on the trans", I'll pick the first scenario..because for what it costs to rebuild / replace a trans,...you can buy a LOT of gasoline.
I notice you say your usage is 'mostly city'. If it's stop / go, or even stoplight to stoplight - the best thing you can do to make the trans last longer - is an external transmission cooler. They cost about the same as a tune, and are a lot cheaper than rebuilding a trans. Outside of that, your conditions don't sound too bad (e.g.; no towing, doesn't sound like you drive too aggressively, etc.) Also, if you're stoplight-to-stoplight - you probably don't get the chance to even get your TC to lockup, as I've been writing about above.
Anyway, let us know how you like your tune when you get it back. As I mentioned above - I just sent my PCM out for a tune (mostly for fan codes, but also to 'wake up' the throttle response - which you should notice as well, if you're having Torque Mgmt eliminated outright ('0%')).