Huh? Can you cite where they "worked to emphasize" anything of the sort? There's an entire, 12-page, illustrated section on "PAINTING MINIATURES" in Total Warfare. I get that people have some attachment to using proxies, but how that's being superimposed over the rule book, I have no idea. In fact, using counters in place of 'Mechs is only mentioned once in the book, that I've read.
Phrased slightly better, what I should have said was "They have really worked to emphasis how they aren't as necessary in the Total Warfare era." Specifically, in the rule book, you are correct. But it has certainly been mentioned in public much more in this current era of product than in prior ones. Both GenCons I attended, line developers spoke on this in public. I've heard multiple different Commandos/Agents who have spoken about this with players. You have a great deal of access to top-down images easily used for cardstock proxy printing via certain programs. Most of the canon events I've played in after the release of TW featured proxies (albeit, mini proxies rather than WYSIWYG) far more than the previous Martial Olympiads and previous tournament style events. You don't need to look far on the forums to see a writer or developer talking to a new/returning player about how easy it is to get back into the game, and how minis are not necessary. Off the top of my head (as I no longer have older rules editions to check anymore), I don't recall other editions even having the simple boilerplate that TW does.
You're correct, it isn't likely prolific in the community. It certainly isn't promoted at the default. But any amount of promotion for proxy capabilities is a lot more than previously found in the larger community pre-TW. To be fair, that's simply been my experience. That's not meant as a statement of fact, simply what I've noticed.
You CAN use counters or pennies or whatever else. Absolutely nothing wrong with that, whatsoever. Minis are expensive and not everyone has hundreds of $$$ to buy a full set. But it's a stretch to say BT is intended to be played without minis. That's why I had suggested a small "Era Pack" of plastic minis for each era. For example, the Clan Invasion would have one of each OmniMech. The Jihad could have a "Celestials" special edition or "Word of Blake" mini-set. If you can't afford $15 for one mini, it might be affordable to pay $30 for 12 and get some real bang for your buck.
Personally, I'd much rather see them put the money into some solid cardstock printable proxy image PDFs similar to Reinforcements back in the day. Some of the small, micro-releases have seen some solid success with other (non-minis) game companies, particularly Posthuman Studios as an example. I have no idea how this would work in relation to the legalities of licenses regarding IWM, CGL, and Topps. But seeing how they've struggled time and again with the minis for box sets, I'd really love to see some support offered for the budget-restricted player. I think this would be an excellent edition to Alpha Strike, but that may just be me.