Flex - I don't know. It's covered by rear panel / cosmetic cover. My mounting is, uh, suboptimal. I'm reusing the 1/16th inch think cosmetic plastic protector ring from the factory sub as a spacer, and sealing with a couple layers of 3/8" foam. I am under no illusion this is an SPL perfect type setup, it'll have a some flex and might have some leaks too. I did find a 1/2" piece of plywood under my deck last weekend, so I'll roll a spacer ring at some point. All these compromises in place it sounds good, so can only improve. The ring/spacer I'm using is meant to keep the rear panel off the factory sub cone.
Signal boosters/LOCs: I am using the factory 2 channel low level signal available under the driver seat on connector F18. It is also available behind the head unit. No signal boosters or LOCs. My situation is pretty unique, as I have fully replaced the Mark Levinson amplifier. It failed, I didn't see spending $500 on a rebuild or $1400 for a new one, so I'm on the third iteration of replacement solution, and second DSP solution (still less than $1400 all in for all iterations, though it is getting close, or course I have way more power . . . to do it this way without having to iterate is around $700, anyhow . . .). So I use the Factory HU/DVD/CD player (and 1/8" input) as sources. The 2 channel low level carries all the signals the HU sees (DVDA, DVDV, CD, FM, Aux, etc). Current DSP also has a separate BT input, but like a lot of BT implementations it has its own set of issues. The DSP creates the 12 channels of output (same as Mark Levinson amp did) with appropriate time delay and frequency ranges, then either DSP or external amp drive the speakers. The DSP is amplifying five channels (hatch, rear tweeters, center), and I have 7 channels in two 4 channel small form factor digital amps (rear woofers, front woofers, front tweeters, and sub bridged). The DSP is rated 25W, the SFF amps are 90W into 4ohm and 125W into 2 ohm, though I doubt very much they make these rms figures. They are better than the DSP amp for sure. I'll eventually move the sub to a dedicated sub amp (I have a SFF four channel from a previous iteration that I can put in the rear and run bridged, one side to each voice coil on the sub). At that time I'll remount the sub to a better spacer, rewire the VCs for the new amp, and fix the speaker wire gauge issue.
For signal analysis I've been using the DSP software in conjunction with an old school SPL meter and an iOS based sound generator. It's not perfect for sure, but I can do basic things like pink noise leveling by speaker to set master and amp gains, pair leveling, total system measurements etc. I'd like to do some frequency specific matching to better set crossovers and get some of the coloration out of the woofers and tweeters, perhaps I'll play with this on a future weekend. The factory system has built in midrange/tweeter crossovers that I can't control, but I do think I can address some of the coloration. Right now the limiting speakers are the rear tweeters, then center channel as far as power goes. When I move the sub to the third amp I can fix one of those two. Probably will choose the tweeters. The center is pretty close to the listening position and an easy load.