Agreed all the way around.
I know the factory amp has its own built in low pass filter but I have never bothered to look into where it occurs. What occurs to me however, is that both the Boston and Infinity should have a broader frequency range than the cheapy factory units. Stated another way, I doubt the factory units will go as low as either of the potential replacements. So I dare say, both will work fine. Add to this the tendency of the human ear, especially in middle-aged men, to be sensitive to mid-bass frequencies, and it is possible that some drop-out at around 100 Hz may have an equalizing effect. Also, we don't know what order the low pass follows (how steep it is): is it akin to a 3rd, 4th or 5th order Butterworth at 6, 12 or 18 dB per octave or what? This will affect the magnitude of any drop-out at the point of the cross-over. It would also be useful to know what the resonant frequency of the door mid-bass units is or is going to be. Quite a few 6.5 inch drivers hover in the 80 Hz range, so there is significant extra energy still present by 100 Hz. This gives the warm quality to male vocals in a number of speakers using 6.5 inch drivers.
And the 3.5 inch speakers do make some difference, but smaller so than the others. I know that extended frequency response up top, over that provided by the factory units, is definitely noticeable and welcome, especially in verts with the top down.
IMHO, given the cost of decent quality 3.5 in. upgrades, they are a good bang for the buck as an audio upgrade. When not upgrading amplification, I use sensitivity as my first criterion, overall frequency response as number 2, reputation of the manufacturer and my affinity for its other products as number 3, and cost as the deciding factor when it gets down to a two or three way tie. (It is assumed that as a first order of business one has already determined the proper nominal impedances which will be satisfactory and anything not within that range has been rejected).
I know I used to agonize about stuff like this when I was younger. It is easier now. Free market competition has weeded out the truly incompetent and the basics are well understood and executed by all the major players. And I do not care as much as I used to. My experience has been that, following the plan above, most name brands will swap in and give some noticeable improvements.