The process you describe is certainly what happened from about season 3 and going forward.
In Season 1 (and maybe season 2?) the graphics look noticeably different. For one, the font used at the start of the show for LCARS displays was Compacta, rather than the Helvetica Ultracompressed. Comptacta is a font created by Letraset.
After a brief dive into font history... The LaserWriter printer had a small set of Postscript Type 1 fonts built in (including Helvetica) - high quality scalable fonts like that were unique to Postscript devices at the time (in 1985 the LaserWriter was the first), and I'm not sure if there was a way to get that printer to output additional fonts like Compacta, or if an electronic format of that font even existed until later. There were other electronic publishing methods at the time of course but they were not "desktop." Long story short, I have doubts that the art department would have been able to output Compacta through electronic means.
The LCARS screens are also somewhat simpler, with slight misalignments between some letters and elements (as if hand laid, albeit very skillfully). At the least, the "positives" used to generate the translights were assembled by hand from smaller pieces of text and curved shapes - see the crooked "TARGET ACQUISITION" here:
More slightly off-kilter text "EMERGENCY OVERRIDE" (also note the "390" Letraset applied directly to the power button):
The lines of numbers here look slightly out of line vertically from one character to the next, and some UI element corners are out of square (chart tape not cut squarely?):
My proposal of how it worked is this: Interface elements would be trimmed from black stock with straight edge/french curve and arranged to create the overall layout of a translight "positive". Then, using the Letraset Compacta dry transfers, some master sheets were created with long tables/strings of numbers and some phrases that would look good on controls (40271 and other repeated smaller font size number sequences appear all over the place).
These master patterns would be duplicated and smaller portions would be trimmed out and arranged on the translight positive over the interface elements to create pieces of data tables and control labels, along with chart tape for the smaller blocky details (as on the transporter panel above) etc etc. Then, shoot the negative translight, and proceed as Ryan described