Drag to reorder in the list first; the list order is the output order.
A sideways page inside a portrait document reads as a mistake even when it is not.
Confirm the page count and flip to the first page of each source file.
Each source file keeps its own page dimensions. Put an A4 contract and an A3 drawing into one PDF and you get a file where page 1 is 210x297mm and page 2 is 297x420mm. That is a valid PDF and every reader opens it, but a thumbnail strip looks broken and anything assuming a uniform page size will struggle.
The common case is mixed A4 portrait and landscape: a scanned table, or a signed page photographed sideways. The file is fine; the reading experience is not, because the reader has to rotate the device. Rotating the offending page before merging is usually the whole fix.
There is no lossless way to make a mixture of page sizes uniform, because scaling a page means either cropping content or adding margins. The practical route is to print to PDF at A4 with fit-to-page, which produces a uniform document at the cost of turning text into images on the scaled pages. Do that for a print job, not for a file you will edit.
The merged output follows the list order, so fix the sequence before merging. Reordering afterwards means merging again from scratch; this toolset has no way to move a page inside a finished file.
Only by rasterising: print to PDF at A4 with fit-to-page. Text on scaled pages becomes an image.
Slightly. Each source keeps its own resources and nothing is deduplicated.
No. Decrypt it first, then merge.