Yeah, Machine Empires feel pretty borked. You need insane amounts of micromanagement, edict-running, pre-planning, pop-optimizing and penny pinching to barely eke out a living. The amount of work that would see you become the richest bastard in the universe with a fleshy empire and have you rolling in triple-digit income can barely keep machine empires afloat. And sometimes even that won't save from dipping into red in your baseline energy or even crystal production, because you need to funnel those into pop production as well.
And even if you do all of that, there is simply no pay-off. You start painfully slow - your robot pops grow slower than bio pops (which makes no sense to me, surely it's faster to cobble together a machine than it is to make a baby and wait until it's born and reaches majority?), you early game mineral production is abysmal because from day1 they are being consumed for pop production, your early research/unity/alloy/whatever production is abysmal because you can't afford to run any of those buildings - all of your slooowly spwaning pops are needed to run the basic energy and mining districts to keep your head above water in basic resource production. You also need a dedicated building slot and workers to actually grow your population, for added insult, further putting you behind every biological civilization, who certainly don't need to build "breeding centers" and assign workers to them to get growth going.
You are literally at your neighbor's mercy for a very, very long time because you can't physically afford to actually do anything, besides grow at an abysmal pace and pray they won't decide to attack you and wipe you out, which they can at virtually any point and there is nothing you can do to stop it. And of course this is all the more likely to happen because everyone hates you by default for your government type. Your early game literally consists of waiting and praying. You are also much more screwed by the available planets around you. A couple of garden worlds with heavy emphasis on farming districts, or worlds with heavily blocked energy tiles? Congratulations - you are screwed, while a biological civ can easily work around that and generate credits through trade.
And even after you slog through all that crawling early game, if by luck you didn't get attacked and conquered, after you robomod your pops and manage to claw your way to relevancy (by which time you could have become a local superpower with a biological pop with the same amount of effort) ... well, it's not like there exists any real payoff. Machine Worlds, when you finally manage to get them up and running, are kinda nice but it's not like they will actually boost you enough to help you overtake the biological pops. More like they will put you on equal footing, finally ... except your start is abysmal compared to theirs, so you are still behind regardless. Where's the payoff for playing an empire that has worse relations with everyone by default and can't take advantage of commerce?
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Frankly, Machine Empires need two things to become more than an exercise in masochism - an increased pop build speed and the ability to take advantage of commerce. It makes no sense that they can't in the first place - why can't they derive value from the same random asteroids and planetoids that biological pops extract commerce from? Surely there's minerals or compounds there the machines would find valuable for some function or other? And why in the world can't you trade with biologicals? Surely the galaxy-spanning AI can comprehend the benefits of engaging in exchange with the biologicals and bringing in those sweet duracell batteries that it is in such a desperate need for? Engaging in trade to get stuff it needs surely isn't beyond the concept of an AI to grasp?
Commerce can be lucrative as hell - you can easily work up to 4-digit numbers in terms of income from it. That's a huge load of almost-free energy that biological empires get to take advantage of, while machines have no equivalent to it, and this is probably where much of the huge economic disparity comes from.
I love playing as empires, I love playing as megacorps, I used to love playing as machines as well ... but as of right now they are simply not on the same scale as everyone else in the game, and whereas everyone else can have meaningful early game choices and interactions, a 2.2 Machine Empire early game is the most abysmal experience I have ever had in Stellaris, and the feeling of having started out as a gimped cripple never really goes away. Did they even test this state of balance before shipping it? Because I would be very surprised if the answer is anything but a flat "no".
) makes it feel like you are going bankrupt because you are, in fact, trying to do too much with too little.