Not a bug report I think, this issue seems to be a result of implementation and everything is working as intended as far as I can tell:
Blueprinting Payloaders with circuit control is, as far as I see, impossible, since the entities that you can read the contents of don't exist until after they're placed, so circuit connections won't be placed when the blueprint is first loaded. I suppose you could work around this by having staged blueprints, but it's still rather annoying. One way to fix this issue would be to make it so you can read the contents of the input container from the main entity.

Additionally, the Payloader seems... very limited. I've only dabbled in Factorio modding briefly, that is to say I am unsure what's possible or feasible to implement. I think it would be much better if the Payloader acted as a single entity. Having an input slot dedicated to the Payload Vehicle, and a number of slots equal to the slots available in the Vehicle displayed beneath it. Finally, an output slot like a normal recipe in any other machine for inserters to take from. If you want to balance out buffing the Payloader in this way, its crafting speed could be determined by the number of items / item stacks you're inserting per craft. I've attached an image for a mock-up of the UI:

[img]https://cloud.astragroup.info/core/preview?fileId=3664887&x=1440&y=900&a=true&etag=e1923b6d53d93e9946a6d8beae5129ea[/img]

Not a bug report I think, this issue seems to be a result of implementation and everything is working as intended as far as I can tell:
Blueprinting Payloaders with circuit control is, as far as I see, impossible, since the entities that you can read the contents of don't exist until after they're placed, so circuit connections won't be placed when the blueprint is first loaded. I suppose you could work around this by having staged blueprints, but it's still rather annoying. One way to fix this issue would be to make it so you can read the contents of the input container from the main entity.

Additionally, the Payloader seems... very limited. I've only dabbled in Factorio modding briefly, that is to say I am unsure what's possible or feasible to implement. I think it would be much better if the Payloader acted as a single entity. Having an input slot dedicated to the Payload Vehicle, and a number of slots equal to the slots available in the Vehicle displayed beneath it. Finally, an output slot like a normal recipe in any other machine for inserters to take from. If you want to balance out buffing the Payloader in this way, its crafting speed could be determined by the number of items / item stacks you're inserting per craft. I've attached an image for a mock-up of the UI:

https://cloud.astragroup.info/core/preview?fileId=3664887&x=1440&y=900&a=true&etag=e1923b6d53d93e9946a6d8beae5129ea

edit: okay I can't get the image to embed, apologies

Hello again!

In regards to blueprinting, yes, this is an issue that I've been thinking on, but don't presently have a good solution for other than staged/phased blueprints as you suggest at present. Ideas welcome.

As far as reading the Payloader's containers from the main entity/having it as a single standard "crafting-machine" type entity: this sadly isn't possible as far as I understand (at least given current API limitations), as a normal "crafting-machine" takes a standard recipes inputs, and outputs the recipes outputs; the bind here is, via recipe prototypes, an item cannot be physically placed into its inventory, even if the type of the output item is "item-with-inventory". This is why the Payloader has the extra invisible containers, as a means of providing the requisite inputs, and finished output, such that it can dynamically load/unload a given PV at runtime without the hassle of trying to create unique prototypes for all possible combinations and/or permutations.

Hope that helps. Let me know if have any other questions, ideas, or suggestions!

Hm. That's unfortunate, I take it there's no way to make a generic entity? The idea there being to side-step the recipe system and have a custom entity that just runs the script when it's told to. It would probably require having 2 different entities, the Payloader and the "Unpayloader"/"Payunloader" (I think those names would be very amusing). I don't think the machines being separate would be too big of a deal, especially if there's a recipe that allows you to convert one to another with just the opposite machine as input.