I get around dealing with save-scumming and other unfun tactics by roleplaying it. The way I see it, if a faction is willing to sell me giant guns and enormous capital ships and I'm a faction hero that knows many higher ups personally, they'll let me commission their shipyards to make things for me at a premium (1x to 2x price, depending on rarity/class). There are limits to this, naturally, but as long as I have access to a sizable faction planet anything common is up for commissioning. Construction time is based off of Omnifactory times for lack of proper lore to work with.
The exceptions are as follows:
1. Prototype/special ships E.G. Excalibur, Snow Goose: Given that these usually have highly sensitive and proprietary equipment, I only let myself commission these if I own a significant faction shipyard (Nexerelin player faction). If I own the shipyard, the answer is "yes your majesty," not "no, you well-regarded free agent."
2. Unbuildable ships E.G. XIV-class, IBB bounties: These ships simply can't be commissioned, since there's no ability to construct them. If I have access to a large, trustworthy, friendly market and the ship is a class (XIV-akin), I'll strip something around to 3x-5x the normal purchase price from my credits, and start rolling low-probability dice each week for my ongoing (presumably advertised) bid to bear fruit. If it's totally unique I'm basically SOL until it comes up for sale somewhere. I don't go in for gamey tactics like buying out a market completely. I can use the bid system for common ships that I can't access shipyards for, but the downsides are obvious.
On the upside, I get guaranteed vessels of classes I want, on the downside it costs money and time. I figure it's fair. With luck there will be a shipyard commissioning ability when industry matures more from regular factions, and an ability to do some construction of your own with high-level outposts and industry commitment. Fingers crossed, anyway.