Your concern is quite valid. And while I cannot, and do not, speak for the team, here's my view to the whole thing.
The M3 milestone was more than just successful. It blew all funding expectations. But more than just the funding, it brought a lot of new people into the fold, and the $1 and $5 packs played a very important role in achieving that.
Here's a reminder of the rewards for the $1 pack:
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The amount of rewards, and their quality, can be compared to stuff that can be found in high-tier founder packs for most other early access games.
The one important thing that's missing though? Access to the game on release.
The whole point of the new upgrade system is so that lower tier M3 backers who may not have had the chance to buy the higher tier packs (those that give access to the game, lowest one being the Deepscanner) do get a chance to do so. And with the program running until Kickstarter launch (about 3 months) that's a lot of time they have, to opt into buying access to the game for a much lower price than what would be on release.
Further, do remember that the new purchase options are not open to everyone, only M3 backers. It would have been quite easy for the team to open up the plan for everyone. To be honest, there are quite a few who would have gladly bought one of the packs, since several people missed the M3 milestone session and have been clamoring for an opportunity to back the game, somehow someway. It's quite likely that the team would have easily doubled the M3 returns by opening up the funding options to everyone. And yet, it's open only to M3 backers.
Furthermore, the bike is free with any and all upgrades, including an upgrade to the Scout perkpack ($15). That's a $14 for a few more rewards and the bike. Upgrade to Deepscanner and that's the bike, plus access to the game, for $34 (assuming you upgrade from the $1 tier). Seeing as the game is to be priced at the higher end of indie pricing at release, that's a lot of value for investment there.
Anyone who has funded the M3 milestone do get access to a bike, the original M3 two-seater. As for the new Python, true it does play on the nostalgia factor a bit, but it's just an option for those that can afford to, and want to, invest a bit more into a game that they feel was stolen from them.
The way I see it, for a team that's working part time and depending entirely on the community, they have played things right so far. They have met targets, albeit delayed at times, but that's to be expected, and the rewards they have offered are far more value for money than most other early access games on the market.
I'd say keep the faith. The community and the team have known each other for a significant amount of time. I'm sure the team knows that the community will be on their backs if they start to step out of line, just as they know the community will back them through thick and thin.