The pH number that matters
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Everything about how your sauce is regulated, processed and stored follows from one number, and the number is 4.6.
4.6, and why
Clostridium botulinum cannot grow and produce toxin below roughly pH 4.6. That single fact is why the regulatory line sits there and why so much of what you have to do is organized around proving which side of it you are on.
Producers often target well below 4.6 rather than at it, commonly at or under 4.0, because the line is a limit and not a goal. Ingredients vary, measurement has error, and a batch aimed exactly at the line has nowhere to be wrong.
Equilibrated pH is the measurement
Not the pH of the mix as you stir it. The pH after the acid has fully distributed through the product, which takes time and which a thick or chunky sauce reaches more slowly than a thin one.
Measuring too early gives a reassuring number that the finished product does not have. Pockets of low-acid material inside a thick sauce can sit above the line while the reading at the surface is fine, which is exactly the failure the rules are written around.
Measure with a calibrated meter, not paper strips. Strips are not adequate for a decision with this consequence, and a meter that has not been calibrated that day is a meter reporting its own drift.
Acidified versus naturally acid
The distinction decides which regulations apply to you.
A naturally acid food is below 4.6 on its own. A acidified food is one with low-acid ingredients, peppers, garlic, onion, carrot, brought below 4.6 by adding acid, usually vinegar. Most hot sauces are acidified, and many producers assume they are not.
Being acidified brings a set of federal requirements with it: registration, a scheduled process established by a process authority, operator training, and processing records. Those are not optional and they are not something a state cottage food exemption sets aside.
What this makes you
Say the inconvenient part plainly. If you are making a vinegar-based sauce with peppers, garlic and onion, you are very likely a manufacturer of acidified foods, and the path runs through a process authority rather than through a market stall.
That is a real cost and a real delay, and it is cheaper than the alternative. It is also a common thing small producers discover late, usually when a retailer or an inspector asks for a scheduled process number they do not have.
Equilibrium, not the reading at the end of the cook
The number in the regulation is a finished equilibrium pH: the pH after the acid has finished moving through everything in the bottle, solids included.
Which is why a reading taken while the pot is still hot and the pieces are still firm is not the number that matters. The measurement that counts is taken on the finished, equilibrated product, and the time it takes to get there is one of the things the process specifies.
A chunky sauce equilibrates slowly. A smooth one equilibrates quickly. Two formulas at the same nominal pH can be in completely different positions an hour after filling.
Why filings usually sit under 4.6
4.6 is the regulatory ceiling, not a target. Meters drift, batches vary and solids are not uniform, so a process written at the ceiling has no margin in it at all.
Process authorities routinely specify a maximum below it for that reason, and your scheduled process rather than the regulation is the number you are actually held to. If your letter says 4.0, then 4.2 is a deviation even though the regulation would have allowed it.
Read your own maximum off the letter and put that number on the batch sheet. Writing 4.6 there because that is the number everybody quotes is how a batch passes the form and fails the process.