Allowing fictional players or career minor leaguers into MLB changes the talent in the league. However ratings alone can't produce realistic league output with all historical players so League Total Modifiers are used to make the total output correct.
When the talent changes the total league output is still hammered into historical totals even if the talent means the totals should be different. This changes the performance of all players.
For more information on how this works see
THIS THREAD and don't buy the obfuscation and misinformation posted by Garlon.
For the best chance of historical players performing historically, do not allow fictional players or career minor leaguers into MLB. Players who play longer than they did historically also affect the talent pool but I've found the effect is tolerable.
Do not play with League Total Modifiers fixed and not tested against the league. The rating system AND historical LTMs still will not produce historical output. The game tests and changes the modifiers to work before the season.
Supposedly the effect of LTMs is lessened in 25 due to improved ratings (according to Matt) while Garlon says the use of LTMs has been expanded and the game will never be able to run without them. So there's a disagreement between God the OOTP Father and God the OOTP Son.