I think you are talking about "drop-outs" rather than "skips". Unless your ld-decode methodology is flawed or underpowered. And there are certainly "drop-outs" in this capture, you can clearly see them in the video I posted above.
In order to attempt to remedy this, the (DomesDay) process is called "stacking" where you basically "compare" multiple disk captures (you really need a minimum of 4 captures, from 4 different disks) and if a defect is detected, the other members of the "stack" are checked. If the defect is on all of them, it's a mastering error, if it's not then it's a capture defect and is discarded from that source and the other source members are used for that frame.
Ultimately it's all about maintaining the best "perfect" frames and framerate to ensure your end result is a playable media on real hardware, or in true emulation. The current single capture seems to play fine and is frame accurate in the MPEG as far as I am able to tell on all the scene skips (i.e. no "skips" as frames are accurate).
It may be a little premature to start working from a single exported LDF sources, with lossless conversions (it's actually lossy) from radio frequency analog sources to digital MKV. For stacking to occur, you will always have to refer back to the LDF/TBC RF captures. As only 400 copies of this LE disk were produced and who knows how may no-rotted copies remain, it might be a long or even fruitless wait.
If you just wanna work from "the best we currently have" then sure, use the current single source, ultimately you are altering the source material with your cleanup in any case, so no purist is ever going to want to use it, lossless or not, and it certainly won't be accepted in MAME. But in lesser emulators it should be a great addition.
DomesDay documentation is very well written.