In the Pull Request, https://github.com/Blood-Asp/GT5-Unofficial/pull/1544 , some players objected to no longer being able to pull from input hatches or push into output hatches. This made no sense to me when I assumed they were talking about doing it with automation (e.g. pump covers on the input hatches). However, further comments clarified that they are apparently instead using the hatches as a workaround for the lack of a manual, non-powered way to empty fluid containers into single-block machines' input tanks and fill them from single-block machines' output tanks.
If I'm understanding Leagris's most recent comment correctly, both draknyte1's PR and my "improved" version are apparently pointless, but let me try again to respond to the summary points:
1. "Fix single-block machines and GUI to allow free input output of fluids" - I looked a bit more into this, and there isn't really room for leaving fluid containers next to the input/output tanks. I haven't found where they're actually handled, so idk whether I could add in-gui "click to fill/empty" functionality, but I might be able to add a way to fill the input tank with a held fluid container or fill an empty held fluid container from the output tank. Edit: I've added the in-gui "click to fill/empty" functionality (in a fork, Pull Request not started yet), though I haven't added a tooltip or anything to make it clear that you can do that. I haven't entirely decided whether to still add the in-world interaction, but I can deal with that after I've had some sleep. Edit 2: probably not worthwhile.
2. "Fix machines to only have to deal with a single copy of a recipe using fluids regardless of contained or raw fluid." - nice idea, but tricky to implement, especially when you think about outputting empty cells afterward.
3. "Fix remove the now useless plunger." - The plunger is kind of useless now, given that you can wrench the machine to completely clear the input tank (as opposed to what, 1000L at a time with the plunger?), but might not remain useless - see below.
4. "Fix remove the now useless fluid canner." - There are a few special and non-reversible recipes in the fluid canner - batteries (fluid redstone, sulfuric acid, or mercury) and coolant (for use in nuclear reactors), plus inserting/removing the cells or other fluid containers can be automated. (Edit 3: that is less unique to the fluid canner than I thought; input/output hatches allow this, though with restrictions on which sides allow automated input/output, plus there's quantum tanks, and the cheaper tanks from GT++) I have to vote against removing it completely.
5. "Fix machines to keep their inventories, power, state on harvest." - nice idea, but could make the plunger less useless, and machines that have such state would no longer easily stack in a processing array.